[BioC] Different RMA expression values in different BioC versions?

[James W. MacDonald]

Quanli Wang wrote:
>>Different than what? An earlier version with the same chips?
> 
> Yes. For the same chips using justRMA, the values from R2.3.1/BioC1.8 will 
> be very different from that from R2.4.0/BioC1.9.
> Quanli

I don't see that here. I get identical results for the same chips using 
these two versions of R/BioC

 > eset <- justRMA()
Background correcting
Normalizing
Calculating Expression
 > save(eset, file="eset2.3.1.Rdata")
 > sessionInfo()
Version 2.3.1 (2006-06-01)
i386-pc-mingw32

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils" 
     "datasets"
[8] "base"

other attached packages:
hgu133plus2cdf           affy         affyio        Biobase
       "1.12.0"       "1.10.0"        "1.0.0"       "1.10.1"

[close R-2.3.1, start R-2.4.0]

 > eset2 <- justRMA()
Background correcting
Normalizing
Calculating Expression
 > load("eset2.3.1.Rdata")
 > all.equal(exprs(eset), exprs(eset2))
[1] TRUE
 > sessionInfo()
R version 2.4.1 (2006-12-18)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils" 
"datasets"  "methods"
[8] "base"

other attached packages:
hgu133plus2cdf           affy         affyio        Biobase
       "1.14.0"       "1.12.2"        "1.2.0"       "1.12.2"

Can you show the code you used to get different results, and the output 
of sessionInfo(), as requested in my last email?

Best,

Jim


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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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