[BioC] AffyID mapping question

[Marc Carlson]

Hi Jiayi,

If you 1st upgrade to a modern version of R, then you should be able to 
do stuff like this:

library(mouse4302.db)
keys = c("1415670_at", "1415671_at", "1415672_at")
cols(mouse4302.db)
keytypes(mouse4302.db)
select(mouse4302.db, keys= keys, cols=c("SYMBOL","CHRLOC"), 
keytype="PROBEID")


Please let us know if you need more help,

   Marc



On 07/02/2012 04:41 AM, Jiayi Hou [guest] wrote:
> I am working on a project trying to mapping Affymetrix probeset ID to Entrez ID, Gene Symbol and its chromosomal location. I used R package biomaRt and another one named mouse4302.db for Affymetrix Mouse430 2.0 array specifically. I noticed from the result, for genes have multiple probesets attached, only a small proportion of these probesets have a precise transcription start locations. While most of these probesets share the same start location with the given gene. Is there anyway I can get a better match in terms of the precise transcription start location for each probeset?
>
>   -- output of sessionInfo():
>
> R version 2.12.2 (2011-02-25)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] mouse4302.db_2.4.5   org.Mm.eg.db_2.4.6   RSQLite_0.10.0
> [4] DBI_0.2-5            AnnotationDbi_1.12.1 mouse4302cdf_2.7.0
> [7] affy_1.28.1          Biobase_2.10.0       biomaRt_2.6.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.18.0         preprocessCore_1.12.0 RCurl_1.5-0.1
> [4] tools_2.12.2          XML_3.2-0.2
>
> --
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>
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