[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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