No it will have no effect. MM's have not actually been used by that code in at least 5 years (or perhaps more). Ben > Ben, > > Thank you very much! That really clarified things. > > I have one last question, regarding to the rma2.C code, will removal of > the vestigial references to MM change RMA results as well? (Oct 28, 2007 > comment.) > > Thanks again. > And Happy Holidays! > > Yiwen > > -----Original Message----- > From: bmb at bmbolstad.com [mailto:bmb at bmbolstad.com] > Sent: Tuesday, December 23, 2008 1:50 PM > To: He, Yiwen (NIH/CIT) [C] > Cc: Davis, Sean (NCI); Ben Bolstad; bioconductor at stat.math.ethz.ch > Subject: RE: [BioC] affy package RMA results difference from R2.5 to R2.8 > > A lot of the C code that was previously in affy (and affyPLM) got moved > off into preprocessCore for easier maintainability. That is where you will > find the quantile normalization code (qnorm.c). In this movement much of > how rma() did its underlying processing was re-factored. But none of those > changes should have made any appreciable difference to the output of the > algorithm. > > My experience with the aforementioned change to the quantile normalization > code is that changes are typically in the forth or fifth significant digit > (on the log scale) in any expression values generated. > > Ben > > > > > >> 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 at 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 at="" mail.nih.gov<mailto:heyiwen="" at="" 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 at bmbolstad.com<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<mailto: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<mailto: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_IDENTIFICA TION=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 at stat.math.ethz.ch<mailto:bioconductor at="" 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 at stat.math.ethz.ch<mailto:bioconductor at="" 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 at stat.math.ethz.ch<mailto:bioconductor at="" stat.math.ethz.ch=""> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > >