[BioC] Possible problem with Rhesus array annotation package

[Marc Carlson]

Hi Andrew,

On closer examination this problem is because certain kinds of 
information are being search for by annaffy that are just not available 
for org.Mmu.eg.db.  The kinds of information being searched for that are 
not found are: ENTREZID (this is actually present but is failing the 
check because this information is normally called "EG" in all of the org 
style packages), MAP and UNIGENE.  The annaffy software is performing a 
check and then when it does not find these kinds of annotation if throws 
the error message that you observed.  So there is nothing actually wrong 
with the annotations, they just don't contain certain specific kinds of 
data (that annaffy was expecting to find).


   Marc


On 07/21/2011 03:02 PM, Marc Carlson wrote:
> Hi Andrew,
>
> I am not completely sure why aafGO() is claiming otherwise, but there
> definitely *is* data in the Mmu organism package.  In a pinch, you can
> always access it generically with simple operations like this:
>
> library("org.Mmu.eg.db")
> ## lets make a feke top table for illustration purposes
> tt<- data.frame(gene_id = c("574097", "574098", "574099"), value= c(1:3))
> tt
>
> ## now suppose that we want to attach the pubmed IDs to that.
> ## We could just attach it using merge() and the PMID mapping for rhesus
> just like this
>
> merge(tt, toTable(org.Mmu.egPMID), by.x="gene_id", by.y="gene_id")
>
>
> Hope this helps,
>
>
>     Marc
>
>
>
> On 07/20/2011 01:51 PM, blockaa at huskers.unl.edu wrote:
>> 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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>>
>>
>>
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