On Tue, Jul 30, 2013 at 9:14 AM, Feng Tian <fengtian@bu.edu> wrote:

> Hi Levi,
>
> Thanks for your reply very much.
> My purpose is to do GSEA analysis. So is there a general way to handle
> these "_x" probes?
>
> Regards,
> Feng
>

After mapping, I would just drop anything with "///" for GSEA analysis. I
suppose you could also choose one representative, or if you are using the
Broad's tool, provide probe sets and let it deal with the mapping (although
I don't know how it deals with non-specific probe sets).  I doubt such
probe sets will have much effect on GSEA results, since most of those genes
will have a more specific probeset available.  E.g.:

> library(hgu133plus2.db)
> x=as.character(hgu133plus2SYMBOL)
> length(x)
[1] 41293   #probe sets
> length(unique(x))
[1] 19944   #gene symbols
> ind=grep("_x", names(x))
> summary(x[ind] %in% x[-ind])
   Mode   FALSE    TRUE    NA's
logical     623    2469       0
>

So for hgu133plus2 you would lose 623 out of 19944 genes - IMO if that
changes your GSEA in an important way, it probably wasn't a robust result
anyways.






>
> On Tue, Jul 30, 2013 at 9:00 AM, Levi Waldron <lwaldron.research@gmail.com
> > wrote:
>
>> Hi Feng,
>>
>> probe sets labelled with "_x" cross-hybridize to multiple genes:
>>
>> http://www.affymetrix.com/support/help/faqs/mouse_430/faq_8.jsp
>>
>> Genecards gives more detail for this probe set:
>>
>>
>> http://genecards.weizmann.ac.il/cgi-bin/geneannot/GA_search.pl?keyword_type=probe_set_id&array=HG-U133&target=genecards&keyword=200012_x_at
>>
>> How to handle such a case depends on how interested you are in that probe
>> set; at the extremes you could ignore it, or follow up with PCR to
>> establish which transcript you are observing.
>>
>> -Levi
>>
>>
>> On Mon, Jul 29, 2013 at 6:06 PM, Feng Tian <fengtian@bu.edu> wrote:
>>
>> > Dear all,
>> >
>> > In the Affymetrix annotation file, I find that some probe set ID are
>> mapped
>> > to multiple genes separated by '///', such as 200012_x_at is mapped
>> > to RPL21P16///RPL21P119///RPL21. How to handle this case?
>> >
>> > Thank you!
>> >
>> > Feng
>> >
>> >         [[alternative HTML version deleted]]
>> >
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>> >
>>
>>
>>
>> --
>> Levi Waldron
>> Post-doctoral fellow
>> Department of Biostatistics, Harvard School of Public Health
>> Department of Biostatistics and Computational Biology, Dana-Farber Cancer
>> Institute
>> Building 1, room 412C
>> 655 Huntington Avenue
>> Boston, Massachusetts 02115
>> mobile: (617) 851-6849
>> fax: (617) 432-5619
>> http://www.hsph.harvard.edu/research/levi-waldron/
>>
>>         [[alternative HTML version deleted]]
>>
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>
>

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