Try 'mogene10sttranscriptcluster.db' ...
On 12-Feb-10, at 4:29 AM, mike dewar wrote:
Hi,
I'm trying to map probeset IDs onto GO terms. I've pulled out the
probeset IDs using the following commands:
cdf <- AffymetrixCdfFile$byChipType("MoGene-1_0-st-v1",tags="r3")
probe_ids <- getUnitNames(cdf, units=attr(geneSumm,"unitGroupCellMap")
[,"unit"])
as per the tutorial. (Must admit to not understanding the
units=attr.... bit). The MoGene cdf file used here is the one
available via your website at http://bioinf.wehi.edu.au/folders/mrobinson/CDF/MoGene-1_0-st-v1,r3.cdf
.
The names in `probe_ids` seem reasonable, and correspond nicely to the
platform data I can pull off GEO for the data set I'm studying
(GPL6246 - the platform used by the Immgen project at Harvard). So,
due to this correspondence, I'm confident in these IDs.
My next step is to pull some functional annotations from the Gene
Ontology database, corresponding to the genes in my happily pre-
processed dataset. This step has proven weirdly elusive. However, I
thought ny troubles were over when I stumbled across the BioC package
'mogene10stprobeset.db' which, although being labelled "Affymetrix
Human Gene 1.0-ST Array Revision 4 annotation data" (http://
www.bioconductor.org/packages/devel/data/annotation/html/mogene10stprobeset.db.html)
at least had a comforting looking filename, in that "mogene10st" sort
of looks like "MoGene-1_0-st" (also googling the name of the package
seems to associate it with our little friend Mus Musculus). However,
if I make a variable called `xx` which contains the 189489 mapped keys
in mogene10stprobeset.db, look what happens:
sum(probe_ids %in% names(xx))
[1] 56
56 is a lot smaller than I had hoped, indicating a lack of
correspondence between the mogene10stprobeset.db and the platform data
on GEO and the cdf file I have pulled from the aroma.affy website. So
maybe this database is for humans after all, or the change from r3 to
r4 has changed all but 56 probe IDs.
So my first question is: in the above, where am I going wrong? Is it
simply that I shouldn't be trying to use Human Gene annotation data to
extract information about mice (despite the hopeful looking filename
and my blind faith in bioinformaticians)?
My second question is: how should I actually go about this? Is there a
cure to my naivety, or is this mapping from probeID to GO term
generally a Hard Thing To Do That Requires Learning Perl and MySQL?
Apologies if the answer to both these problems is "this isn't an
aroma.affymetrix problem" - any help on where else to ask this
question that won't generate an "this isn't an X problem" for X in
['BioC', 'Immgen', 'GO', 'GEO'] would be greatly appreciated.
Cheers,
Mike Dewar
--
When reporting problems on aroma.affymetrix, make sure 1) to run the
latest version of the package, 2) to report the output of
sessionInfo() and traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google
Groups "aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
------------------------------
______________________________________________________________________
The information in this email is confidential and intended solely for the
addressee.
You must not disclose, forward, print or use it without the permission of the
sender.
______________________________________________________________________
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
