[BioC] SE in RMA and GCRMA
davide at microarrays.unife.it
Mon Sep 20 17:05:14 CEST 2004
I had the same problem with GCRMA, and this remind me another, more general,
question... It's possible (and how it is possible) to control GCRMA
procedure, and to have the different outputs (as in the other methods)?
I wasn't able to find answers in the documentation, and on the web too, for
the present version of GCRMA.
Thanks in advance,
----- Original Message -----
From: "Florence Combes" <florence.combes at paris7.jussieu.fr>
To: <bioconductor at stat.math.ethz.ch>
Sent: Monday, September 20, 2004 3:13 PM
Subject: [BioC] SE in RMA and GCRMA
> Dear all,
> My goal is to obtain the standard errors of the signals given by RMA and
> - for RMA, I used
> the function expresso [background correction= rma, normalization=
> quantiles, PM correction= PMonly, expression= medianpolish ] and then
> the se.exprs() one.
> I obtained a matrix with coefficients for each genes on each array.
> My first question is: are these coefficients in log2 base or not ?
> - for GCRMA, I did the same, with the command gcrma() instead of
> expresso() of course, and it seems that I cannot obtain the SE
> coefficients (I have "NA" everywhere).
> So my second question is: is it possible to obtain SE of the signals given
> by GCRMA and, if yes, how ?
> Thanks a lot,
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
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