Thanks Sean, I didn't see the c code in the source at first.

So I was looking at the rma2.c scripts from affy 1.14 (R2.5, BioC2.0), 1.16 (R2.6, BioC 2.1) and 1.18 (R 2.7, BioC 2.2).
Between 1.14 and 1.16, there is this comment:
** May 24, 2007 - median_polish code is now from preprocessCore package

Between 1.16 and 1.18, there are these comments:
 ** Oct 26, 2007 - add verbose flag
 ** Oct 28, 2007 - remove any vestigial references to MM
 ** Mar 31, 2008 - use rma background correction from preprocessCore

I didn't see any mentioning of quantile normalization handling ties. Am I looking at the right place? Looks to me that these documented changes would not affect the results. Ben could you please provide some insights?

Thank you so much!

Yiwen
________________________________
From: Davis, Sean (NCI)
Sent: Tuesday, December 23, 2008 1:12 PM
To: He, Yiwen (NIH/CIT) [C]
Cc: Ben Bolstad; bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] affy package RMA results difference from R2.5 to R2.8


On Tue, Dec 23, 2008 at 1:02 PM, He, Yiwen (NIH/CIT) [C] <heyiwen@mail.nih.gov<mailto:heyiwen@mail.nih.gov>> wrote:
Hi Ben,

I tried to look at the rma code, but looks like the rma.R is a wrapper for the C-code. How do I go further to look at the code where quantile normalizaton actually happened?

That is available in the package source download.

Sean


Thank you very much!

Yiwen

-----Original Message-----
From: Ben Bolstad [mailto:bmb@bmbolstad.com<mailto:bmb@bmbolstad.com>]
Sent: Tuesday, December 23, 2008 9:08 AM
To: balag Ganesan
Cc: He, Yiwen (NIH/CIT) [C]; bioconductor@stat.math.ethz.ch<mailto:bioconductor@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@mail.nih.gov<mailto: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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch<mailto:Bioconductor@stat.math.ethz.ch>
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>       [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch<mailto:Bioconductor@stat.math.ethz.ch>
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch<mailto:Bioconductor@stat.math.ethz.ch>
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


	[[alternative HTML version deleted]]

