[BioC] SE in RMA and GCRMA

Zhijin Wu zwu at jhsph.edu
Tue Sep 21 16:49:57 CEST 2004

the SE frome expresso is not a good choice. One can use affyPLM to get SE.
For rma you can use fitPLM. It is a little complicated with gcrma right
now that you need to background correct with gcrma, then use
fitPLM with background=FALSE

On Mon, 20 Sep 2004, Florence Combes wrote:

> 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,
> Florence.
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