[BioC] PLIER -- low values?

[James MacDonald]

You can simply convert to natural scale yourself. 

exprs(eset) <- 2^exprs(eset)

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> "Tarun Nayar" <tnayar at bcgsc.ca> 05/27/05 5:29 PM >>>
Hi,
 
I've been trying to use PLIER to pre-process microarray data from 5 Rat
230A chips.
 
After using the justPlier function, I get an exprSet, but all of the
probe set intensities are below 12. When I've used PLIER previously with
the same data set(with Affy's free ArrayAssist Lite program), values are
much higher. I'm assuming there is some kind of a log function happening
in the R version. Is there any way to turn the log function off? I've
looked through the options but can't find anything that seems to make
this happen. We're presently using R to compare some data with a
collaborator who is using ArrayAssist.
 
Thanks,
 
Tarun Nayar
Genome Sciences Centre
Vancouver, BC

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