[BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene

Mikhail Pachkov 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)

Best regards,


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