[BioC] SE in RMA and GCRMA
Florence Combes
florence.combes at paris7.jussieu.fr
Mon Sep 20 15:13:53 CEST 2004
Dear all,
My goal is to obtain the standard errors of the signals given by RMA and
GCRMA.
- 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,
Florence.
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