Hello BioConductor list,


I am fairly new to BioConductor. I am working with Affymetrix GeneChip Rhesus Macaque Genome Array. I am able to analysis my data, but I am not able to annotate the results using annaffy and annotate.   I am using org.Mmu.eg.db as the annotation package. Part of the package seems to be missing. I am able to annotate a human array, so I don't think it is my code.  My code (after analysis) is:


> library("annaffy")

> library("annotate")

> source("http://www.bioconductor.org/biocLite.R")

BioC_mirror = http://bioconductor.org

Change using chooseBioCmirror().

> biocLite("org.Mmu.eg.db")

Using R version 2.13.0, biocinstall version 2.8.4.

Installing Bioconductor version 2.8 packages:

[1] "org.Mmu.eg.db"

Please wait...


Installing package(s) into ‘C:/Users/Andrew Block/Documents/R/win-library/2.13’

(as ‘lib’ is unspecified)

trying URL 'http://bioconductor.org/packages/2.8/data/annotation/bin/windows/contrib/2.13/org.Mmu.eg.db_2.5.0.zip'

Content type 'application/zip' length 17734284 bytes (16.9 Mb)

opened URL

downloaded 16.9 Mb


package 'org.Mmu.eg.db' successfully unpacked and MD5 sums checked


The downloaded packages are in

C:\Users\Andrew Block\AppData\Local\Temp\Rtmp36zrGk\downloaded_packages

> library("org.Mmu.eg.db")


> genenames <- as.character(toptable$ID)

> atab <- aafTableAnn(genenames, "org.Mmu.eg.db", aaf.handler())

Error in get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) :

object 'org.Mmu.egORGPKG' not found

In addition: Warning message:

In chkPkgs(chip) :

The org.Mmu.eg.db package does not appear to contain annotation data.


> traceback()

5: get(paste(gsub(".db", "", chip), "ORGPKG", sep = ""))

4: get(paste(gsub(".db", "", chip), "ORGPKG", sep = ""))

3: aafGO(probeids, chip)

2: aaf.handler(probeids, chip, colnames[i])

1: aafTableAnn(genenames1, "org.Mmu.eg.db", aaf.handler())


> sessionInfo()

R version 2.13.0 (2011-04-13)

Platform: i386-pc-mingw32/i386 (32-bit)


attached base packages:

[1] stats graphics grDevices utils datasets methods base


other attached packages:

[1] org.Mmu.eg.db_2.5.0 annotate_1.30.0 annaffy_1.24.0

[4] KEGG.db_2.5.0 GO.db_2.5.0 RSQLite_0.9-4

[7] DBI_0.2-5 AnnotationDbi_1.14.1 rhesuscdf_2.8.0

[10] limma_3.8.2 affy_1.30.0 Biobase_2.12.1


loaded via a namespace (and not attached):

[1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.0

[4] xtable_1.5-6


Thank you for the help in advance.

Andrew Block

Nebraska Center of Virology
University of Nebraska at Lincoln

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