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

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

Hi,

Thank you both for your replies!

Is it safe to say, that a change from '259.2365 and 244.2026' to '259.2308 and 244.2079' in linear space, is small enough to be caused by this change in quantile normalization only, but nothing else? Out of my 22K probes, I have about 1000 probes that changed at that scale, and the rest at a smaller scale.

I looked at the BioC webpage, and saw this: "BioC 2.1 was released on 8 October, 2007 and is designed for R 2.6.z." So it's probably arround that release that the change happened.

Thanks for your clarification.

Yiwen



-----Original Message-----
From: Ben Bolstad [mailto:bmb at bmbolstad.com]
Sent: Tuesday, December 23, 2008 9:08 AM
To: balag Ganesan
Cc: He, Yiwen (NIH/CIT) [C]; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] affy package RMA results difference from R2.5 to R2.8

The only change to the functionality of the rma() algorithmic code in
the last two 18 months or so was in how the quantile normalization
handles ties (looking in code comments this occurred around Jul 2007).
This should only cause small changes in expression values.

Ben


On Mon, 2008-12-22 at 12:44 -0700, balag Ganesan wrote:
> 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 at 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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> >
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