[BioC] problem with chromosome location in annotations WAS: search archives and annnotate questions

[Diego Díez]

Dear all,

I have been building annotation packages for Codelink platform these days
and found this problem exist, but only in the human arrays. No
chromosome locations are found. The annotations created for both mouse
and rat arrays have the  corresponding chromosome locations. At the
first time I was thinking on a problem with my mapping between codelink
ids and genbank ids (recently changed a bit) in the human arrays but now
I realize that it could be a more general problem. This is the
corresponding information about my system:

> sessionInfo()
Version 2.3.0 (2006-04-24)
i686-pc-linux-gnu

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices"
"utils"
[7] "datasets"  "base"

other attached packages:
        GO AnnBuilder    RSQLite        DBI   annotate        XML   
Biobase
  "1.12.0"   "1.10.0"    "0.4-1"   "0.1-10"   "1.10.0"  
"0.99-7"   "1.10.0"

I have and old build from Mon Jan 16 06:53:47 2006 that has the
corresponding chromosome location but I don't have information about
sessionInfo(), only that it was built for R-2.2.0. If you need any other
information let me know.

Any help on this will be very appreciated.

Best regards,

Diego.

>Why is it that so many probesets are annotated with respect to chromosome and cytoband, but >not to "chromosome location" in the annotation packages? I recently performed an analysis using >rat2302 (ver.1.12.0) and passed the results on to a colleague, who subsequently told me that he >has found locations for quite a few of the probesets with location "zero" at the Affy website.
>
>I tried to see if this question has been addressed before but ran into the following problems:
>1. the search button on the Bioconductor homepage is not working (Firefox 1.5.1).
>2. the searchable archives site I used to use has been shut down (http://files.protsuggest.org/cgi->bin/biocond.cgi).
>3. I am not sure how to Goggle just the BioC archives (https://stat.ethz.ch/pipermail/>bioconductor/).
>
>Help in these areas would be appreciated.
>
>Thanks,
>
>Mark W. Kimpel MD 
>
>
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