[BioC] using fitPLM weights in limma analysis

Tom Price tom at spirit.gcrc.upenn.edu
Tue May 11 16:31:27 CEST 2004

I am analysing Affy chip data for differential expression. Previously I have
done this using the 'limma' package without weighting the data. More recently I
have been assessing quality control using the weights from the affyPLM command
fitPLM, which I have found to show up spatial variation on Affy chips very
clearly. I would like to use these weights in the subsequent analysis. Does it
make any sort of sense to feed the affyPLM weights into the limma lm.series
analysis? Alternatively, is there some way to use the limma eBayes technique on
the fitPLM output?

Tom Price: telephone +1 215 898 0489

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