[BioC] getting normexp (and log2 transformed) values - not further-processed M values

adoty at umd.edu adoty at umd.edu
Mon Oct 5 03:20:11 CEST 2009

Dear Listserv,

I have an unusual microarray data set -a RIP-ChIP data set- and would like to use the "normexp" function (as found in limma) to background-subtract my data (and I'll take it's log2 data transformation, too) - but I don't want the automatic M and A value output that you can get from limmaGUI.  [This is solely because my data are not the least bit normal and I cannot use limma to analyze them further.] 

Is there a way for me to obtain the normexp (and transformed) data from within R?  Is is an "object" that I can "print" or "write" before it gets converted to M values? 

Thank you very much for your help,

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