Hi,

On Monday, July 2, 2012, 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.


Can you clarify what you mean by a "transcription start location" for a
probeset? Is this A function of the probes themselves? Or are you talking
about the TSS of the gene that the probeset's probes land in.

If it's the latter are these different TSS's just different annotated TSS's
of different isoforms of the genes?


>  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?


I guess I don't understand what you mean by the "start location" of a
probeset -- perhaps you can clarify a bit more what you are trying to do?
Perhaps more details about the problem you are trying to solve would also
be helpful.


>  -- output of sessionInfo():
>
> R version 2.12.2 (2011-02-25)
> Platform: i386-pc-mingw32/i386 (32-bit)


Thanks for also including your sessionInfo output -- while we're trying to
sort this out, you might take this opportunity to upgrade your version of R
to the latest (2.15.1) since we don't really try to support outdated
versions of bioc packages.

HTH,

-Steve


> 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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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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