Interesting.We shifted from R2.2 to 2.6 mid-this year for one of our systems
and notice o such difference at all.
BALA

On Mon, Dec 22, 2008 at 12:07 PM, He, Yiwen (NIH/CIT) [C] <
heyiwen@mail.nih.gov> wrote:

> 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
>
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