[BioC] affy package RMA results difference from R2.5 to R2.8

[He, Yiwen (NIH/CIT) [C]]

Hi,

We have been using R 2.5 and affy 1.14.0 from BioConductor 2.0 release. Recently, we updated our R/BioC versions to R 2.8/BioC2.3, and I noticed that the RMA results from affy package rma() are slightly different.

For example, I have a gene whose summarized values (in linear space) were 259.2365 and 244.2026 in the older version, but are 259.2308 and 244.2079 in the newer version.

Although the difference for this gene is not big, other genes have differences at a much smaller scale.

I haven't tested R2.6 and R2.7, but I know that R2.4 and R2.5 gave me identical results.

I'm wondering if there is any change in the way rma is calculated in the new affy packages.

Here are my code and seesionInfo:

> eset <- rma(myData)
> exprs(eset) <- 2^exprs(eset)

> sessionInfo()
R version 2.5.0 (2007-04-23)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=C;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
    affy   affyio  Biobase
"1.14.0"  "1.4.0" "1.14.0"


> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] affy_1.20.0   Biobase_2.2.1

loaded via a namespace (and not attached):
[1] affyio_1.10.1        preprocessCore_1.4.0


Thank you for your help!

Yiwen