Answer: justPlier outputs negative values
Hi Burak -
I'm a newbie with Bioconductor and R, so I don't know whether this
I executed 'justPlier()' on several data sets on which I was somewhat
familiar. I compared results with those I obtained using mas5 and
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
executed the program incorrectly, perhaps choosing inadequate options,
etc. However, with limited time, I chose, temporarily, to NOT use the
Sorry to sound so pessimistic. Perhaps some other members on the list
can provide more assistance.
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
E-Mail gwa at css.ncifcrf.gov
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of burak
Sent: Sunday, October 01, 2006 12:42 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] justPlier outputs negative values
I am analyzing affy data with 'justPlier()' and there are some
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?
Version 2.3.1 (2006-06-01)
attached base packages:
 "tools" "methods" "stats" "graphics" "grDevices"
 "datasets" "base"
other attached packages:
plier affy affyio Biobase
"1.4.0" "1.10.0" "1.0.0" "1.10.0"
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