[BioC] justPlier outputs negative values

[Alvord, Greg (DMS) [Contr]]

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 at 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"


 		
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