Welcome to the NuGO R-server!

Latest modifications

30 September 2009:

Added Affymetrix annotation libraries for the GeneTitan plates (see Table 3 below).
Added MBNI Custom CDF annotation libraries (version 12.0.0) for the GeneTitan plates (I added them to Table 4 below).

Bioconductor support libraries for NuGO

On this page, you can find R/Bioconductor libraries for Unix/Linux and Windows:
1. Bioconductor support libraries for the human and mouse NuGO arrays.
2. Bioconductor annotation libraries for the Affymetrix Gene Titan system.
3. Custom Chip Definition Files (CDFs) for the human and mouse NuGO arrays.
4. Custom Chip Definition Files (CDFs) for all other supported human, mouse, and rat species (annotation libraries only).

Remark on installing the NuGO array support files:
For a single species, you need to download three files: the annotation, cdf, and probe packages. For example: mmnugomm1a520177mmentrezg_9.0.1.zip, mmnugomm1a520177mmentrezgcdf_9.0.1.zip, and mmnugomm1a520177mmentrezgprobe_9.0.1.zip for the NuGO customCDF mouse arrays.

The custom CDF files are identical to the ones from the MBNI website, EXCEPT that the annotation libraries are complete (instead of containing only the genenames). That is the reason why all available human, mouse and rat Custom CDF annotation libraries (for Bioconductor) are available for download here.

REMARK: we decided to use the ENTREZ Custom CDF-files for the following reasons:

Most up-to-date.
Corresponds to genes (not transcripts).
Accepted input for follow-up analyses.

Off course, you are free to use one of the other formats, e.g. ENSEMBL, but I will not supply Bioconductor annotation libraries for those custom CDFs.

Installation instructions

For Windows: download the appropriate .zip-files from the tables below. In R, go to Packages => Install package(s) from local zip-files... Browse to the location where you downloaded your .zip-files and select the files you want to install. Done!

For Unix/Linux: download the appropriate .tar.gz files from the tables below. cd to the directory where you downloaded your .tar.gz files and execute the following command (multiple times for multiple .tar.gz files): R CMD INSTALL <your downloaded.tar.gz file>.

Download tables

1.Human and mouse NuGO array support files (Affymetrix CDF; standard; .db annotation approach).
The probe and CDF-libraries are the same as under table 6. The annotation packages are rebuilt using the .db annotation approach (but using the same input files as version 1.0.4).

Affymetrix array type	Linux/Unix	Windows	Supported R/BioC versions
Human NuGO Array (nugohs1a520180)	nugohs1a520180.db_1.0.5.tar.gz	nugohs1a520180.db_1.0.5.zip	>=R-2.7.0 and >=Bioconductor-2.2
Human NuGO Array (nugohs1a520180)	nugohs1a520180cdf_1.0.4.tar.gz	nugohs1a520180cdf_1.0.4.zip	>=R-2.7.0 and >=Bioconductor-2.2
Human NuGO Array (nugohs1a520180)	nugohs1a520180probe_1.0.4.tar.gz	nugohs1a520180probe_1.0.4.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mouse NuGO Array (nugomm1a520177)	nugomm1a520177.db_1.0.5.tar.gz	nugomm1a520177.db_1.0.5.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mouse NuGO Array (nugomm1a520177)	nugomm1a520177cdf_1.0.4.tar.gz	nugomm1a520177cdf_1.0.4.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mouse NuGO Array (nugomm1a520177)	nugomm1a520177probe_1.0.4.tar.gz	nugomm1a520177probe_1.0.4.zip	>=R-2.7.0 and >=Bioconductor-2.2

2. Human and mouse NuGO array support files (VERSION 12.0.0; MBNI Custom CDF; 2 August 2009).
Here, also the CDF and PROBE libraries are available for download. To obtain full NuGO array support, you need to download and install all three libraries for each species!

Affymetrix array type	Linux/Unix	Windows	Supported R/BioC versions
Human NuGO array (nugohs1a520180)	nugohs1a520180hsentrezg.db_12.0.0.tar.gz	nugohs1a520180hsentrezg.db_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Human NuGO array (nugohs1a520180)	nugohs1a520180hsentrezgcdf_12.0.0.tar.gz	nugohs1a520180hsentrezgcdf_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Human NuGO array (nugohs1a520180)	nugohs1a520180hsentrezgprobe_12.0.0.tar.gz	nugohs1a520180hsentrezgprobe_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Mouse NuGO array (nugomm1a520177)	nugomm1a520177mmentrezg.db_12.0.0.tar.gz	nugomm1a520177mmentrezg.db_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Mouse NuGO array (nugomm1a520177)	nugomm1a520177mmentrezgcdf_12.0.0.tar.gz	nugomm1a520177mmentrezgcdf_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Mouse NuGO array (nugomm1a520177)	nugomm1a520177mmentrezgprobe_12.0.0.tar.gz	nugomm1a520177mmentrezgprobe_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4

3. Affymetrix annotation libraries for the GeneTitan plate arrays (ht* arrays). I named it to version 12.0.0 to make it in agreement with the CustomCDF annotation libraries (30 September 2009).
The reason is that I will update all annotation libraries at the same time, so utilizing the same version numbers is more convenient. The cdf and probe libraries are available
at the Bioconductor website. The hthgu133a.db and hthgu133b.db libraries INCLUDES the Affymetrix control probes (as opposed to the official Bioconductor packages)!

Affymetrix array type (GeneTitan plates)	Linux/Unix	Windows	Supported R/BioC versions
Human: Gene Titan hgu133a plates (hthgu133a)	hthgu133a.db_12.0.0.tar.gz	hthgu133a.db_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Human: Gene Titan hgu133a plates (hthgu133b)	hthgu133b.db_12.0.0.tar.gz	hthgu133b.db_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Human: Gene Titan hgu133pluspm plates (hthgu133pluspm)	hthgu133pluspm.db_12.0.0.tar.gz	hthgu133pluspm.db_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Mouse: Gene Titan mg430a plates (htmg430a)	htmg430a.db_12.0.0.tar.gz	htmg430a.db_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Mouse: Gene Titan mg430b plates (htmg430b)	htmg430b.db_12.0.0.tar.gz	htmg430b.db_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Mouse: Gene Titan mg430pm plates (htmg430pm)	htmg430pm.db_12.0.0.tar.gz	htmg430pm.db_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Rat: Gene Titan ratfocus plates (htratfocus)	htratfocus.db_12.0.0.tar.gz	htratfocus.db_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4
Rat: Gene Titan rat230pm plates (htrat230pm)	htrat230pm.db_12.0.0.tar.gz	htrat230pm.db_12.0.0.zip	>=R-2.9.1 and >= BioC-2.4

4. Annotation libraries for the MBNI Custom CDF annotation files (VERSION 12.0.0; updated 30 September 2009).
The CDF and PROBE libraries are available at the MBNI website. To obtain full Custom CDF support, you need to download and install all three libraries for each species!

Affymetrix array type	Linux/Unix	Windows	Supported R/BioC versions
Arabidopsis thaliana (ath1121501attairg)	ath1121501attairg.db_12.0.0.tar.gz	ath1121501attairg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Arabidopsis thaliana (tilingatsnptilx520433attairg)	tilingatsnptilx520433attairg.db_12.0.0.tar.gz	tilingatsnptilx520433attairg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo sapiens hgfocus	hgfocushsentrezg.db_12.0.0.tar.gz	hgfocushsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo sapiens hgu133a2	hgu133a2hsentrezg.db_12.0.0.tar.gz	hgu133a2hsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo sapiens hgu133a	hgu133ahsentrezg.db_12.0.0.tar.gz	hgu133ahsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo sapiens hthgu133a (GeneTitan plates)	hthgu133ahsentrezg.db_12.0.0.tar.gz	hthgu133ahsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo Sapiens hgu133b	hgu133bhsentrezg.db_12.0.0.tar.gz	hgu133bhsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo sapiens hthgu133b (GeneTitan plates)	hthgu133bhsentrezg.db_12.0.0.tar.gz	hthgu133bhsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo Sapiens hgu133plus2	hgu133plus2hsentrezg.db_12.0.0.tar.gz	hgu133plus2hsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo sapiens hthgu133pluspm (GeneTitan plates)	hthgu133pluspmhsentrezg.db_12.0.0.tar.gz	hthgu133pluspmhsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo Sapiens hgu95av2	hgu95av2hsentrezg.db_12.0.0.tar.gz	hgu95av2hsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo Sapiens hgu95b	hgu95bhsentrezg.db_12.0.0.tar.gz	hgu95bhsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo Sapiens hgu95c	hgu95chsentrezg.db_12.0.0.tar.gz	hgu95chsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo Sapiens hgu95d	hgu95dhsentrezg.db_12.0.0.tar.gz	hgu95dhsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo Sapiens hgu95e	hgu95ehsentrezg.db_12.0.0.tar.gz	hgu95ehsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo sapiens 133x3p	u133x3phsentrezg.db_12.0.0.tar.gz	u133x3phsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo sapiens hugene10stv1	hugene10stv1hsentrezg.db_12.0.0.tar.gz	hugene10stv1hsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Homo sapiens huex10stv2	huex10stv2hsentrezg.db_12.0.0.tar.gz	huex10stv2hsentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus mgu74av2	mgu74av2mmentrezg.db_12.0.0.tar.gz	mgu74av2mmentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus mgu74bv2	mgu74bv2mmentrezg.db_12.0.0.tar.gz	mgu74bv2mmentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus mgu74cv2	mgu74cv2mmentrezg.db_12.0.0.tar.gz	mgu74cv2mmentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus moe430a	moe430ammentrezg.db_12.0.0.tar.gz	moe430ammentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus htmg430a (GeneTitan plates)	htmg430ammentrezg.db_12.0.0.tar.gz	htmg430ammentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus moe430b	moe430bmmentrezg.db_12.0.0.tar.gz	moe430bmmentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus htmg430b (GeneTitan plates)	htmg430bmmentrezg.db_12.0.0.tar.gz	htmg430bmmentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus moe430a2	mouse430a2mmentrezg.db_12.0.0.tar.gz	mouse430a2mmentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus mouse4302	mouse4302mmentrezg.db_12.0.0.tar.gz	mouse4302mmentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus htmg430pm (GeneTitan plates)	htmg430pmmmentrezg.db_12.0.0.tar.gz	htmg430pmmmentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus mogene10stv1	mogene10stv1mmentrezg.db_12.0.0.tar.gz	mogene10stv1mmentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Mus musculus moex10stv1	moex10stv1mmentrezg.db_12.0.0.tar.gz	moex10stv1mmentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Rattus norvegicus rae230a	rae230arnentrezg.db_12.0.0.tar.gz	rae230arnentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Rattus norvegicus rae230b	rae230brnentrezg.db_12.0.0.tar.gz	rae230brnentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Rattus norvegicus rat2302	rat2302rnentrezg.db_12.0.0.tar.gz	rat2302rnentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Rattus norvegicus htrat230pm (GeneTitan plates)	htrat230pmrnentrezg.db_12.0.0.tar.gz	htrat230pmrnentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Rattus norvegicus rgu34a	rgu34arnentrezg.db_12.0.0.tar.gz	rgu34arnentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Rattus norvegicus rgu34b	rgu34brnentrezg.db_12.0.0.tar.gz	rgu34brnentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Rattus norvegicus rgu34c	rgu34crnentrezg.db_12.0.0.tar.gz	rgu34crnentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Rattus norvegicus ragene10stv1	ragene10stv1rnentrezg.db_12.0.0.tar.gz	ragene10stv1rnentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Rattus norvegicus raex10stv1	raex10stv1rnentrezg.db_12.0.0.tar.gz	raex10stv1rnentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4
Rattus norvegicus htratfocus (GeneTitan plates)	htratfocusrnentrezg.db_12.0.0.tar.gz	htratfocusrnentrezg.db_12.0.0.zip	>=R-2.9.1 and >=Bioconductor-2.4

5. Human and mouse NuGO array support files (VERSION 11.0.0; MBNI Custom CDF; .db annotation approach; strongly advised!).
Here, also the CDF and PROBE libraries are available for download. To obtain full NuGO array support, you need to download and install all three libraries for each species!
NOTE: compared to the previous custom CDF-versions (<=10.0.0), the Custom CDF annotation library naming scheme has been adapted!!

Affymetrix array type	Linux/Unix	Windows	Supported R/BioC versions
Human NuGO array (nugohs1a520180) Update 28 October 2008 Update 22 July 2009	hsnugohs1a520180hsentrezg.db_11.0.0.tar.gz hsnugohs1a520180hsentrezg.db_11.0.2.tar.gz hsnugohs1a520180hsentrezg.db_11.0.3.tar.gz	hsnugohs1a520180hsentrezg.db_11.0.0.zip hsnugohs1a520180hsentrezg.db_11.0.2.zip hsnugohs1a520180hsentrezg.db_11.0.3.zip	>=R-2.7.0 and >= BioC-2.2 >=R-2.8.0 and >= BioC-2.3 >=R-2.9.0 and >= BioC-2.4
Human NuGO array (nugohs1a520180)	hsnugohs1a520180hsentrezgcdf_11.0.0.tar.gz	hsnugohs1a520180hsentrezgcdf_11.0.0.zip	>=R-2.7.0 and >= BioC-2.2
Human NuGO array (nugohs1a520180)	hsnugohs1a520180hsentrezgprobe_11.0.0.tar.gz	hsnugohs1a520180hsentrezgprobe_11.0.0.zip	>=R-2.7.0 and >= BioC-2.2
Mouse NuGO array (nugomm1a520177) Update 28 October 2008 Update 22 July 2009	mmnugomm1a520177mmentrezg.db_11.0.0.tar.gz mmnugomm1a520177mmentrezg.db_11.0.2.tar.gz mmnugomm1a520177mmentrezg.db_11.0.3.tar.gz	mmnugomm1a520177mmentrezg.db_11.0.0.zip mmnugomm1a520177mmentrezg.db_11.0.2.zip mmnugomm1a520177mmentrezg.db_11.0.3.zip	>=R-2.7.0 and >= BioC-2.2 >=R-2.8.0 and >= BioC-2.3 >=R-2.9.0 and >= BioC-2.4
Mouse NuGO array (nugomm1a520177)	mmnugomm1a520177mmentrezgcdf_11.0.0.tar.gz	mmnugomm1a520177mmentrezgcdf_11.0.0.zip	>=R-2.7.0 and >= BioC-2.2
Mouse NuGO array (nugomm1a520177)	mmnugomm1a520177mmentrezgprobe_11.0.0.tar.gz	mmnugomm1a520177mmentrezgprobe_11.0.0.zip	>=R-2.7.0 and >= BioC-2.2

6. 28 October 2008: Updated annotation libraries for the MBNI Custom CDF annotation files (VERSION 11.0.0; .db annotation approach).
The CDF and PROBE libraries are available at the MBNI website. To obtain full Custom CDF support, you need to download and install all three libraries for each species!

Affymetrix array type	Linux/Unix	Windows	Supported R/BioC versions
Arabidopsis thaliana (ath1121501attaircdf v11.0.0) Arabidopsis thaliana (ath1121501attaircdf v11.0.1) Update 22 July 2009 (ath1121501attairgcdf v11.0.1)	ath1121501attair.db_11.0.2.tar.gz ath1121501attair.db_11.0.3.tar.gz ath1121501attairg.db_11.0.5.tar.gz	ath1121501attair.db_11.0.2.zip ath1121501attair.db_11.0.3.zip ath1121501attairg.db_11.0.5.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo sapiens hgfocus Update 22 July 2009	hgfocushsentrezg.db_11.0.2.tar.gz hgfocushsentrezg.db_11.0.3.tar.gz	hgfocushsentrezg.db_11.0.2.zip hgfocushsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo sapiens hgu133a2 Update 22 July 2009	hgu133a2hsentrezg.db_11.0.2.tar.gz hgu133a2hsentrezg.db_11.0.3.tar.gz	hgu133a2hsentrezg.db_11.0.2.zip hgu133a2hsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo sapiens hgu133a Update 22 July 2009	hgu133ahsentrezg.db_11.0.2.tar.gz hgu133ahsentrezg.db_11.0.3.tar.gz	hgu133ahsentrezg.db_11.0.2.zip hgu133ahsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo Sapiens hgu133b Update 22 July 2009	hgu133bhsentrezg.db_11.0.2.tar.gz hgu133bhsentrezg.db_11.0.3.tar.gz	hgu133bhsentrezg.db_11.0.2.zip hgu133bhsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo Sapiens hgu133plus2 Update 22 July 2009	hgu133plus2hsentrezg.db_11.0.2.tar.gz hgu133plus2hsentrezg.db_11.0.3.tar.gz	hgu133plus2hsentrezg.db_11.0.2.zip hgu133plus2hsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo Sapiens hgu95av2 Update 22 July 2009	hgu95av2hsentrezg.db_11.0.2.tar.gz hgu95av2hsentrezg.db_11.0.3.tar.gz	hgu95av2hsentrezg.db_11.0.2.zip hgu95av2hsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo Sapiens hgu95b Update 22 July 2009	hgu95bhsentrezg.db_11.0.2.tar.gz hgu95bhsentrezg.db_11.0.3.tar.gz	hgu95bhsentrezg.db_11.0.2.zip hgu95bhsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo Sapiens hgu95c Update 22 July 2009	hgu95chsentrezg.db_11.0.2.tar.gz hgu95chsentrezg.db_11.0.3.tar.gz	hgu95chsentrezg.db_11.0.2.zip hgu95chsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo Sapiens hgu95d Update 22 July 2009	hgu95dhsentrezg.db_11.0.2.tar.gz hgu95dhsentrezg.db_11.0.3.tar.gz	hgu95dhsentrezg.db_11.0.2.zip hgu95dhsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo Sapiens hgu95e Update 22 July 2009	hgu95ehsentrezg.db_11.0.2.tar.gz hgu95ehsentrezg.db_11.0.3.tar.gz	hgu95ehsentrezg.db_11.0.2.zip hgu95ehsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo sapiens 133x3p Update 22 July 2009	u133x3phsentrezg.db_11.0.2.tar.gz u133x3phsentrezg.db_11.0.3.tar.gz	u133x3phsentrezg.db_11.0.2.zip u133x3phsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo sapiens hugene10stv1 Update 22 July 2009	hugene10stv1hsentrezg.db_11.0.2.tar.gz hugene10stv1hsentrezg.db_11.0.3.tar.gz	hugene10stv1hsentrezg.db_11.0.2.zip hugene10stv1hsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Homo sapiens huex10stv2 (CDF version 11.0.1!) Update 22 July 2009	huex10stv2hsentrezg.db_11.0.2.tar.gz huex10stv2hsentrezg.db_11.0.3.tar.gz	huex10stv2hsentrezg.db_11.0.2.zip huex10stv2hsentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Mus musculus mgu74av2 Update 22 July 2009	mgu74av2mmentrezg.db_11.0.2.tar.gz mgu74av2mmentrezg.db_11.0.3.tar.gz	mgu74av2mmentrezg.db_11.0.2.zip mgu74av2mmentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Mus musculus mgu74bv2 Update 22 July 2009	mgu74bv2mmentrezg.db_11.0.2.tar.gz mgu74bv2mmentrezg.db_11.0.3.tar.gz	mgu74bv2mmentrezg.db_11.0.2.zip mgu74bv2mmentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Mus musculus mgu74cv2 Update 22 July 2009	mgu74cv2mmentrezg.db_11.0.2.tar.gz mgu74cv2mmentrezg.db_11.0.3.tar.gz	mgu74cv2mmentrezg.db_11.0.2.zip mgu74cv2mmentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Mus musculus moe430a Update 22 July 2009	moe430ammentrezg.db_11.0.2.tar.gz moe430ammentrezg.db_11.0.3.tar.gz	moe430ammentrezg.db_11.0.2.zip moe430ammentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Mus musculus moe430b Update 22 July 2009	moe430bmmentrezg.db_11.0.2.tar.gz moe430bmmentrezg.db_11.0.3.tar.gz	moe430bmmentrezg.db_11.0.2.zip moe430bmmentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Mus musculus moe430a2 Update 22 July 2009	mouse430a2mmentrezg.db_11.0.2.tar.gz mouse430a2mmentrezg.db_11.0.3.tar.gz	mouse430a2mmentrezg.db_11.0.2.zip mouse430a2mmentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Mus musculus mouse4302 Update 22 July 2009	mouse4302mmentrezg.db_11.0.2.tar.gz mouse4302mmentrezg.db_11.0.3.tar.gz	mouse4302mmentrezg.db_11.0.2.zip mouse4302mmentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Mus musculus mogene10stv1 Update 22 July 2009	mogene10stv1mmentrezg.db_11.0.2.tar.gz mogene10stv1mmentrezg.db_11.0.3.tar.gz	mogene10stv1mmentrezg.db_11.0.2.zip mogene10stv1mmentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Mus musculus moex10stv1 (CDF version 11.0.1!) Update 22 July 2009	moex10stv1mmentrezg.db_11.0.2.tar.gz moex10stv1mmentrezg.db_11.0.3.tar.gz	moex10stv1mmentrezg.db_11.0.2.zip moex10stv1mmentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Rattus norvegicus rae230a Update 22 July 2009	rae230arnentrezg.db_11.0.2.tar.gz rae230arnentrezg.db_11.0.3.tar.gz	rae230arnentrezg.db_11.0.2.zip rae230arnentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Rattus norvegicus rae230b Update 22 July 2009	rae230brnentrezg.db_11.0.2.tar.gz rae230brnentrezg.db_11.0.3.tar.gz	rae230brnentrezg.db_11.0.2.zip rae230brnentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Rattus norvegicus rat2302 Update 22 July 2009	rat2302rnentrezg.db_11.0.2.tar.gz rat2302rnentrezg.db_11.0.3.tar.gz	rat2302rnentrezg.db_11.0.2.zip rat2302rnentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Rattus norvegicus rgu34a Update 22 July 2009	rgu34arnentrezg.db_11.0.2.tar.gz rgu34arnentrezg.db_11.0.3.tar.gz	rgu34arnentrezg.db_11.0.2.zip rgu34arnentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Rattus norvegicus rgu34b Update 22 July 2009	rgu34brnentrezg.db_11.0.2.tar.gz rgu34brnentrezg.db_11.0.3.tar.gz	rgu34brnentrezg.db_11.0.2.zip rgu34brnentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Rattus norvegicus rgu34c Update 22 July 2009	rgu34crnentrezg.db_11.0.2.tar.gz rgu34crnentrezg.db_11.0.3.tar.gz	rgu34crnentrezg.db_11.0.2.zip rgu34crnentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Rattus norvegicus ragene10stv1 Update 22 July 2009	ragene10stv1rnentrezg.db_11.0.2.tar.gz ragene10stv1rnentrezg.db_11.0.3.tar.gz	ragene10stv1rnentrezg.db_11.0.2.zip ragene10stv1rnentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4
Rattus norvegicus raex10stv1 (CDF version 11.0.1!) Update 22 July 2009	raex10stv1rnentrezg.db_11.0.2.tar.gz raex10stv1rnentrezg.db_11.0.3.tar.gz	raex10stv1rnentrezg.db_11.0.2.zip raex10stv1rnentrezg.db_11.0.3.zip	>=R-2.8.0 and >=Bioconductor-2.3 >=R-2.9.0 and >=Bioconductor-2.4

7. MBNI Custom CDF annotation files (VERSION 11.0.0; .db annotation approach).
The CDF and PROBE libraries are available at the MBNI website. To obtain full Custom CDF support, you need to download and install all three libraries for each species!
NOTE: compared to the previous custom CDF-versions (<=10.0.0), the Custom CDF annotation library naming scheme has been adapted!!

Affymetrix array type	Linux/Unix	Windows	Supported R/BioC versions
Homo sapiens hgfocus	hgfocushsentrezg.db_11.0.0.tar.gz	hgfocushsentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo sapiens hgu133a2	hgu133a2hsentrezg.db_11.0.0.tar.gz	hgu133a2hsentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo sapiens hgu133a	hgu133ahsentrezg.db_11.0.0.tar.gz	hgu133ahsentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo Sapiens hgu133b	hgu133bhsentrezg.db_11.0.0.tar.gz	hgu133bhsentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo Sapiens hgu133plus2	hgu133plus2hsentrezg.db_11.0.0.tar.gz	hgu133plus2hsentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo Sapiens hgu95av2	hgu95av2hsentrezg.db_11.0.0.tar.gz	hgu95av2hsentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo Sapiens hgu95b	hgu95bhsentrezg.db_11.0.0.tar.gz	hgu95bhsentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo Sapiens hgu95c	hgu95chsentrezg.db_11.0.0.tar.gz	hgu95chsentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo Sapiens hgu95d	hgu95dhsentrezg.db_11.0.0.tar.gz	hgu95dhsentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo Sapiens hgu95e	hgu95ehsentrezg.db_11.0.0.tar.gz	hgu95ehsentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo sapiens 133x3p	u133x3phsentrezg.db_11.0.0.tar.gz	u133x3phsentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus mgu74av2	mgu74av2mmentrezg.db_11.0.0.tar.gz	mgu74av2mmentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus mgu74bv2	mgu74bv2mmentrezg.db_11.0.0.tar.gz	mgu74bv2mmentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus mgu74cv2	mgu74cv2mmentrezg.db_11.0.0.tar.gz	mgu74cv2mmentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus moe430a	moe430ammentrezg.db_11.0.0.tar.gz	moe430ammentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus moe430b	moe430bmmentrezg.db_11.0.0.tar.gz	moe430bmmentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus moe430a2	mouse430a2mmentrezg.db_11.0.0.tar.gz	mouse430a2mmentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus mouse4302	mouse4302mmentrezg.db_11.0.0.tar.gz	mouse4302mmentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Rattus norvegicus rae230a	rae230arnentrezg.db_11.0.0.tar.gz	rae230arnentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Rattus norvegicus rae230b	rae230brnentrezg.db_11.0.0.tar.gz	rae230brnentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Rattus norvegicus rat2302	rat2302rnentrezg.db_11.0.0.tar.gz	rat2302rnentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Rattus norvegicus rgu34a	rgu34arnentrezg.db_11.0.0.tar.gz	rgu34arnentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Rattus norvegicus rgu34b	rgu34brnentrezg.db_11.0.0.tar.gz	rgu34brnentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Rattus norvegicus rgu34c	rgu34crnentrezg.db_11.0.0.tar.gz	rgu34crnentrezg.db_11.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2

8. Human and mouse NuGO array support files (VERSION 10.0.0; MBNI Custom CDF; .db annotation approach; strongly advised!).
The probe and CDF-libraries are the same as under table 9. The annotation packages are rebuilt using the .db annotation approach.
Here, also the CDF and PROBE libraries are available for download. To obtain full NuGO array support, you need to download and install all three libraries for each species!

Affymetrix array type	Linux/Unix	Windows	Supported R/BioC versions
Human NuGO array (nugohs1a520180)	hsnugohs1a520180hsentrezg.db_10.0.0.tar.gz	hsnugohs1a520180hsentrezg.db_10.0.0.zip	>=R-2.7.0 and >= BioC-2.2
Human NuGO array (nugohs1a520180)	hsnugohs1a520180hsentrezgcdf_10.0.0.tar.gz	hsnugohs1a520180hsentrezgcdf_10.0.0.zip	>=R-2.7.0 and >= BioC-2.2
Human NuGO array (nugohs1a520180)	hsnugohs1a520180hsentrezgprobe_10.0.0.tar.gz	hsnugohs1a520180hsentrezgprobe_10.0.0.zip	>=R-2.7.0 and >= BioC-2.2
Mouse NuGO array (nugomm1a520177)	mmnugomm1a520177mmentrezg.db_10.0.0.tar.gz	mmnugomm1a520177mmentrezg.db_10.0.0.zip	>=R-2.7.0 and >= BioC-2.2
Mouse NuGO array (nugomm1a520177)	mmnugomm1a520177mmentrezgcdf_10.0.0.tar.gz	mmnugomm1a520177mmentrezgcdf_10.0.0.zip	>=R-2.7.0 and >= BioC-2.2
Mouse NuGO array (nugomm1a520177)	mmnugomm1a520177mmentrezgprobe_10.0.0.tar.gz	mmnugomm1a520177mmentrezgprobe_10.0.0.zip	>=R-2.7.0 and >= BioC-2.2

9. MBNI Custom CDF annotation files (VERSION 10.0.0; .db annotation approach).
The CDF and PROBE libraries are available at the MBNI website. To obtain full Custom CDF support, you need to download and install all three libraries for each species!

Affymetrix array type	Linux/Unix	Windows	Supported R/BioC versions
Arabidopsis thaliana (ATH1ATTAIR) (Update 5 November 2008)	ath1attair.db_10.0.0.tar.gz ath1attair.db_10.0.1.tar.gz	ath1attair.db_10.0.0.zip ath1attair.db_10.0.1.zip	>=R-2.7.0 and >=Bioconductor-2.2 >=R-2.8.0 and >=Bioconductor-2.3
Homo sapiens HGFOCUS	hsfocushsentrezg.db_10.0.0.tar.gz	hsfocushsentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo sapiens HS133A	hs133ahsentrezg.db_10.0.0.tar.gz	hs133ahsentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo Sapiens HS133AV2	hs133av2hsentrezg.db_10.0.0.tar.gz	hs133av2hsentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo Sapiens HS133B	hs133bhsentrezg.db_10.0.0.tar.gz	hs133bhsentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo Sapiens HGU133PLUS2	hs133phsentrezg.db_10.0.0.tar.gz	hs133phsentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo Sapiens HGU95AV2	hs95av2hsentrezg.db_10.0.0.tar.gz	hs95av2hsentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Homo sapiens U133X3P	hs133xhsentrezg.db_10.0.0.tar.gz	hs133xhsentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus MOE430A2	mm430a2mmentrezg.db_10.0.0.tar.gz	mm430a2mmentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus MOE430A	mm430ammentrezg.db_10.0.0.tar.gz	mm430ammentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus MOE430B	mm430bmmentrezg.db_10.0.0.tar.gz	mm430bmmentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus MOE430PLUS2	mm430mmentrezg.db_10.0.0.tar.gz	mm430mmentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus MGU74AV1	mm74av1mmentrezg.db_10.0.0.tar.gz	mm74av1mmentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus MGU74AV2	mm74av2mmentrezg.db_10.0.0.tar.gz	mm74av2mmentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus MGU74BV2	mm74bv2mmentrezg.db_10.0.0.tar.gz	mm74bv2mmentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Mus musculus MGU74CV2	mm74cv2mmentrezg.db_10.0.0.tar.gz	mm74cv2mmentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Rattus norvegicus RN230A	rn230arnentrezg.db_10.0.0.tar.gz	rn230arnentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Rattus norvegicus RN230B	rn230brnentrezg.db_10.0.0.tar.gz	rn230brnentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Rattus norvegicus RN230	rn230rnentrezg.db_10.0.0.tar.gz	rn230rnentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2
Rattus norvegicus RN34A	rn34arnentrezg.db_10.0.0.tar.gz	rn34arnentrezg.db_10.0.0.zip	>=R-2.7.0 and >=Bioconductor-2.2

10. Human and mouse NuGO array support files (Affymetrix CDF; standard).
Although the libraries are compiled for R-2.5.1/Bioconductor 2.0, it should work fine in R-2.5.0 or R-2.6.0 and Bioconductor 2.0 and 2.1.

Affymetrix array type	Linux/Unix	Windows	Supported R/BioC versions
Human NuGO Array (nugohs1a520180)	nugohs1a520180_1.0.4.tar.gz	nugohs1a520180_1.0.4.zip	>=R-2.5.0 and >=Bioconductor-2.0
Human NuGO Array (nugohs1a520180)	nugohs1a520180cdf_1.0.4.tar.gz	nugohs1a520180cdf_1.0.4.zip	>=R-2.5.0 and >=Bioconductor-2.0
Human NuGO Array (nugohs1a520180)	nugohs1a520180probe_1.0.4.tar.gz	nugohs1a520180probe_1.0.4.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mouse NuGO Array (nugomm1a520177)	nugomm1a520177_1.0.4.tar.gz	nugomm1a520177_1.0.4.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mouse NuGO Array (nugomm1a520177)	nugomm1a520177cdf_1.0.4.tar.gz	nugomm1a520177cdf_1.0.4.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mouse NuGO Array (nugomm1a520177)	nugomm1a520177probe_1.0.4.tar.gz	nugomm1a520177probe_1.0.4.zip	>=R-2.5.0 and >=Bioconductor-2.0

11. Human and mouse NuGO array support files (VERSION 10.0.0; MBNI Custom CDF; strongly advised!).
Although the libraries are compiled for R-2.6.0/Bioconductor 2.1, it should work fine in R-2.5.0 or R-2.5.1 and Bioconductor 2.0.
Here, also the CDF and PROBE libraries are available for download. To obtain full NuGO array support, you need to download and install all three libraries for each species!

Affymetrix array type	Linux/Unix	Windows	Intended R/BioC versions
Human NuGO array (nugohs1a520180)	hsnugohs1a520180hsentrezg_10.0.0.tar.gz	hsnugohs1a520180hsentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Human NuGO array (nugohs1a520180)	hsnugohs1a520180hsentrezgcdf_10.0.0.tar.gz	hsnugohs1a520180hsentrezgcdf_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Human NuGO array (nugohs1a520180)	hsnugohs1a520180hsentrezgprobe_10.0.0.tar.gz	hsnugohs1a520180hsentrezgprobe_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Mouse NuGO array (nugomm1a520177)	mmnugomm1a520177mmentrezg_10.0.0.tar.gz	mmnugomm1a520177mmentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Mouse NuGO array (nugomm1a520177)	mmnugomm1a520177mmentrezgcdf_10.0.0.tar.gz	mmnugomm1a520177mmentrezgcdf_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Mouse NuGO array (nugomm1a520177)	mmnugomm1a520177mmentrezgprobe_10.0.0.tar.gz	mmnugomm1a520177mmentrezgprobe_10.0.0.zip	R-2.6.0 and Bioconductor-2.1

12. MBNI Custom CDF annotation files (VERSION 10.0.0).
Although the libraries are compiled for R-2.6.0/Bioconductor 2.1, it should work fine in R-2.5.0 or R-2.5.1 and Bioconductor 2.0.
The CDF and PROBE libraries are available at the MBNI website. To obtain full Custom CDF support, you need to download and install all three libraries for each species!

Affymetrix array type	Linux/Unix	Windows	Intended R/BioC versions
Homo sapiens HGFOCUS	hsfocushsentrezg_10.0.0.tar.gz	hsfocushsentrezg_10.0.0.zip	R-2.6.2 and Bioconductor-2.1 (!!)
Homo sapiens HS133A	hs133ahsentrezg_10.0.0.tar.gz	hs133ahsentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Homo Sapiens HS133AV2	hs133av2hsentrezg_10.0.0.tar.gz	hs133av2hsentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Homo Sapiens HS133B	hs133bhsentrezg_10.0.0.tar.gz	hs133bhsentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Homo Sapiens HGU133PLUS2	hs133phsentrezg_10.0.0.tar.gz	hs133phsentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Homo Sapiens HGU95AV2	hs95av2hsentrezg_10.0.0.tar.gz	hs95av2hsentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Mus musculus MOE430A2	mm430a2mmentrezg_10.0.0.tar.gz	mm430a2mmentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Mus musculus MOE430A	mm430ammentrezg_10.0.0.tar.gz	mm430ammentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Mus musculus MOE430B	mm430bmmentrezg_10.0.0.tar.gz	mm430bmmentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Mus musculus MOE430PLUS2	mm430mmentrezg_10.0.0.tar.gz	mm430mmentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Mus musculus MGU74AV1	mm74av1mmentrezg_10.0.0.tar.gz	mm74av1mmentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Mus musculus MGU74AV2	mm74av2mmentrezg_10.0.0.tar.gz	mm74av2mmentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Mus musculus MGU74BV2	mm74bv2mmentrezg_10.0.0.tar.gz	mm74bv2mmentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Mus musculus MGU74CV2	mm74cv2mmentrezg_10.0.0.tar.gz	mm74cv2mmentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Rattus norvegicus RN230A	rn230arnentrezg_10.0.0.tar.gz	rn230arnentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Rattus norvegicus RN230B	rn230brnentrezg_10.0.0.tar.gz	rn230brnentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Rattus norvegicus RN230	rn230rnentrezg_10.0.0.tar.gz	rn230rnentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1
Rattus norvegicus RN34A	rn34arnentrezg_10.0.0.tar.gz	rn34arnentrezg_10.0.0.zip	R-2.6.0 and Bioconductor-2.1

13. Human and mouse NuGO array support files (VERSION 9.0.1; MBNI Custom CDF; strongly advised!)
Although the libraries are compiled for R-2.5.1/Bioconductor 2.0, it should work fine in R-2.5.0 or R-2.6.0 and Bioconductor 2.0 and 2.1
Here, also the CDF and PROBE libraries are available for download. To obtain full NuGO array support, you need to download and install all three libraries for each species!

Affymetrix array type	Linux/Unix	Windows	Supported R/BioC versions
Human NuGO array (nugohs1a520180)	hsnugohs1a520180hsentrezg_9.0.1.tar.gz	hsnugohs1a520180hsentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Human NuGO array (nugohs1a520180)	hsnugohs1a520180hsentrezgcdf_9.0.1.tar.gz	hsnugohs1a520180hsentrezgcdf_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Human NuGO array (nugohs1a520180)	hsnugohs1a520180hsentrezgprobe_9.0.1.tar.gz	hsnugohs1a520180hsentrezgprobe_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mouse NuGO array (nugomm1a520177)	mmnugomm1a520177mmentrezg_9.0.1.tar.gz	mmnugomm1a520177mmentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mouse NuGO array (nugomm1a520177)	mmnugomm1a520177mmentrezgcdf_9.0.1.tar.gz	mmnugomm1a520177mmentrezgcdf_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mouse NuGO array (nugomm1a520177)	mmnugomm1a520177mmentrezgprobe_9.0.1.tar.gz	mmnugomm1a520177mmentrezgprobe_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0

14. MBNI Custom CDF annotation files (VERSION 9.0.1).
Although the libraries are compiled for R-2.5.1/Bioconductor 2.0, it should work fine in R-2.5.0 or R-2.6.0 and Bioconductor 2.0 and 2.1
The CDF and PROBE libraries are available at the MBNI website. To obtain full Custom CDF support, you need to download and install all three libraries for each species!

Affymetrix array type	Linux/Unix	Windows	Supported R/BioC versions
Homo sapiens HS133A	hs133ahsentrezg_9.0.1.tar.gz	hs133ahsentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Homo Sapiens HS133AV2	hs133av2hsentrezg_9.0.1.tar.gz	hs133av2hsentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Homo Sapiens HS133B	hs133bhsentrezg_9.0.1.tar.gz	hs133bhsentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Homo Sapiens HGU133PLUS2	hs133phsentrezg_9.0.1.tar.gz	hs133phsentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Homo Sapiens HGU95AV2	hs95av2hsentrezg_9.0.1.tar.gz	hs95av2hsentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mus musculus MOE430A2	mm430a2mmentrezg_9.0.1.tar.gz	mm430a2mmentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mus musculus MOE430A	mm430ammentrezg_9.0.1.tar.gz	mm430ammentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mus musculus MOE430B	mm430bmmentrezg_9.0.1.tar.gz	mm430bmmentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mus musculus MOE430PLUS2	mm430mmentrezg_9.0.1.tar.gz	mm430mmentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mus musculus MGU74AV1	mm74av1mmentrezg_9.0.1.tar.gz	mm74av1mmentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mus musculus MGU74AV2	mm74av2mmentrezg_9.0.1.tar.gz	mm74av2mmentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mus musculus MGU74BV2	mm74bv2mmentrezg_9.0.1.tar.gz	mm74bv2mmentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Mus musculus MGU74CV2	mm74cv2mmentrezg_9.0.1.tar.gz	mm74cv2mmentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Rattus norvegicus RN230A	rn230arnentrezg_9.0.1.tar.gz	rn230arnentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Rattus norvegicus RN230B	rn230brnentrezg_9.0.1.tar.gz	rn230brnentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Rattus norvegicus RN230	rn230rnentrezg_9.0.1.tar.gz	rn230rnentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0
Rattus norvegicus RN34A	rn34arnentrezg_9.0.1.tar.gz	rn34arnentrezg_9.0.1.zip	>=R-2.5.0 and >=Bioconductor-2.0

Concluding remark:

If the annotation library that you need is lacking or if you are using an older version of R/BioC and cannot upgrade: please sent an email to me inquiring about the availability of supported arrays (see the bottom of this page for contact information).

A few words on the new annotation approach (R>=2.7.0 and Bioconductor >=2.2)

As from R-2.7.0 (Bioconductor 2.2), the annotation packages are no longer created as so-called 'environments', but are provided as database (.db) packages utilizing SQLite. That is: in R-2.7.0 (Bioconductor 2.2) you are still allowed to use the 'old-fashioned' environment annotation packages, but you'll get an 'deprecated warning' everytime you use them. In the next R/Bioconductor release, support for annotation environments are simply discarded! Therefore, I recommend to switch to the .db (database) packages. In principle, only minor changes are required for existing scripts to use the new annotation approach. For example, instead of loading e.g. 'library(mouse4302)' you need to call 'library(mouse4302.db)'. That's it! All other functions still work as you are used to because wrappers are available to hide the underlying database commands. For the die-hards: the wrappers have a performance price, as reported in the following snippet from the Bioconductor mailing list (Thu 17 April 2008):

If you want the SQLite-based packages to be close to the same speed as
the environment packages, you probably won't be able to use the
convenience functions that were written to allow naive users to get
similar results with the SQLite packages. Things like get(), mget(), etc
will probably always be slower than a directed SQL query.

> library(GO)
> sam <- sample(ls(GOTERM), 5000)
> system.time(mget(sam, GOTERM))
    user system elapsed
    0.02    0.00    0.02

> library(GO.db)

> sam <- sample(ls(GOTERM), 5000)
> system.time( mget(sam, GOTERM))
    user system elapsed
    5.25    0.02    5.27

> samvec <- paste(paste("'", sam, "'", sep = ""), collapse = ",")
> sql <- paste("SELECT term FROM go_term WHERE go_id IN (",samvec,");")
> system.time(dbGetQuery(GO_dbconn(), sql))
    user system elapsed
    0.09    0.01    0.11

See the vignette in the devel version of AnnotationDbi for more
information about these packages.

Contact:

Dr. Philip de Groot PhD
Nutrition, Metabolism and Genomics group
Division of Human Nutrition
Wageningen University
PO Box 8129
6700 EV Wageningen
The Netherlands
Phone: +31-317-485786
Fax: +31-317-483342
Philip.deGroot@wur.nl

Update history:

2 August 2009:

MBNI Custom CDF version 12 annotation libraries are available now (see Table 4)!
We added support for the Affymetrix tilingatsnptilx520433 array (tilingatsnptilx520433attairg).

22 July 2009:

We updated the annotation libraries for the MBNI CustomCDF version 11. Awaiting the CustomCDF version 12 release, we postponed the creation of new annotation libraries for the current Bioconductor release. However, it turned out that e.g. topGO has problems with the previous annotation libraries because obsolete GO terms are simply discarded which causes topGO to crash. The new annotation libraries (version 11.0.3) do fix this problem. The updated annotation libraries are added in tables 4 and 5 (see below).
MBNI CustomCDF version 12 is being prepared right now. Expect a major update after the holiday season!
From now on, the supported annotation libraries will be updated with each Bioconductor release.
Added a publicly accessible visitors counter (see the bottom of this page).

13 January 2009:

Added MBNI Custom CDF annotation libraries for Affymetrix exon arrays: huex10stv2hsentrezg.db, moex10stv1mmentrezg.db, raex10stv1rnentrezg.db (version 11.0.2; MBNI Custom CDF version 11.0.1)
Updated the Arabidopsis annotation library (ath1121501attair) to version 11.0.3 (depending on MBNI TAIRG Custom CDF version 11.0.1). Some probes were defined multiple times in different probesets. This problem has been corrected by the MBNI Custom CDF version 11.0.1 release. The annotation library for version 11.0.2 remains available, but its use is not recommended!
The entrezg annotation libraries are not affected by the "multiple probes" problem (the problem is not present here), so the MBNI Custom CDF annotation libraries, as listed here, are fully supported in the 11.0.1 release (which is identical to the 11.0.0 release for entrezg).

5 November 2008:

Updated the MBNI Custom Annotation libraries for Arabidopsis (TAIR identifiers) both for version 10.0.0 and version 11.0.0 (see tables 6 and 9 below). These annotation libraries load correctly in R-2.8.0 / Bioconductor 2.3.

28 October 2008:

Updated the MBNI Custom CDF annotation libraries (Entrezgene) to version 11.0.2 (version 11.0.0 of the cdf and probe libraries should still be used).
Added the MBNI Custom CDF annotation libraries for human, mouse, and rat gene 1.0 ST arrays (Entrezg, Table 6).
These updates are intended for R-2.8.0 and Bioconductor 2.3.

22 October 2008:

Fixed a typing error: the name mm74bv2mmentrezg.db_10.0.0.zip is changed to mouse4302mmentrezg.db_11.0.0.zip (Table 7; the underlying link correctly pointed to mouse4302mmentrezg.db_11.0.0.zip). Thanks to Joe Dougherty for reporting this problem.

18 June 2008:

Added the Custom CDF database (.db) annotation libraries for version 11.0.0 (entrezg only).
Moved the text on how to use the .db packages to the bottom of this page.

10 June 2008:

Added the U133X3P homo sapiens .db annotation packages (custom CDF version 10.0.0).

9 June 2008:

Added the Arabidopsis thaliana .db annotation packages (custom CDF version 10.0.0).
Added HGFOCUS homo sapiens annotation packages (both .db and environment packages for custom CDF version 10.0.0).

21 april 2008:

Added the .db annotation packages for R-2.7.0/Bioconductor 2.2.
Added information on the .db packages on top of this document.

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