[BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
pachkov at gmail.com
Mon Mar 22 11:54:34 CET 2010
I have got a problem obtaining probe indices along with probe names. My script:
workingDir = getwd();
pms = pm(rawdata)
res <- dbGetQuery(db(rawdata), "SELECT fsetid,atom,fid FROM pmfeature")
However during analysis of the data it looked like probe names were
determined wrong. I have tried to use pmindex() to extract "fid" of pm
probes which seems to be a list of numbers sorted in ascending order.
I do the following:
# first value in probe names
# first value in pm indices
If I check pgf file for probe with index "1056", it belongs to
probeset "7981328" not "7896737" as it given in pnames.
My question: How to obtain probeset-probe_id pairs in correct order
for annotating expression values in "pms" matrix?
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