[BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
pachkov at gmail.com
Mon Mar 1 11:52:09 CET 2010
On Fri, Feb 26, 2010 at 6:40 PM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> If you're using the latest oligo, you can use the (not exposed - still
> working on further details) function getFidProbeset() :
> probeInfo = oligo:::getFidProbeset(rawdata)
> idx = probeInfo[["fid"]]
> ## probeset names are in probeInfo[["fsetid"]]
> intensities = exprs(rawdata)[idx,]
> and work with 'intensities' (which includes the PMs and controls).
Thank you! It works!
> If you rather use only PMs:
> pms = pm(rawdata)
> pns = probeNames(rawdata)
> these are now regular matrices and you can use
> rma.background.correct() and normalize.quantiles().
Here I have got a problem. probeNames() does not work with my dataset.
pms = pm(rawdata)
pns = probeNames(rawdata)
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: no such column: man_fsetid)
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