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Hi Burak - I'm a newbie with Bioconductor and R, so I don't know whether this helps or hurts. I executed 'justPlier()' on several data sets on which I was somewhat familiar. I compared results with those I obtained using mas5 and rma. I am not qualified to say whether there are bugs in the justPlier program, but I concluded that I did not trust the results. Diagnostic plots, MA-plots, etc., indicated bizarre results. It may be that I have executed the program incorrectly, perhaps choosing inadequate options, etc. However, with limited time, I chose, temporarily, to NOT use the justPlier algorithm. Sorry to sound so pessimistic. Perhaps some other members on the list can provide more assistance. Greg W. Gregory Alvord, Ph.D. Director, Statistical Consulting Services Computer and Statistical Services National Cancer Institute at Frederick Post Office Box B Frederick, MD 21702-1201 Phone: 301.846.5101 Facsimile: 301.846.6196 E-Mail gwa at css.ncifcrf.gov -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of burak kutlu Sent: Sunday, October 01, 2006 12:42 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] justPlier outputs negative values Hi I am analyzing affy data with 'justPlier()' and there are some negative values 9586 out of 427536 values There are some as low as 0.0002 on log2 scale(whatever the default scale of values calculated by justPlier) The PLIER documentation mentions addition of 16 (or 32) to the low values. Is 'justPlier' supposed to that? Is this a bug? Many thanks -burak > sessionInfo() Version 2.3.1 (2006-06-01) i686-pc-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: plier affy affyio Biobase "1.4.0" "1.10.0" "1.0.0" "1.10.0" --------------------------------- Get your email and more, right on the new Yahoo.com [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor