affy package RMA results difference from R2.5 to R2.8
1
0
Entering edit mode
@he-yiwen-nihcit-1177
Last seen 10.2 years ago
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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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_A DDRESS=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
affy affyio affy affyio • 2.4k views
ADD COMMENT •
0
Entering edit mode
balag Ganesan ▴ 140
@balag-ganesan-3020
Last seen 10.2 years ago
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;L C_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_IDEN TIFICATION=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;L C_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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENT •
0
Entering edit mode
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_ID ENTIFICATION=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_IDENTIFICATI ON=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 > > 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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLY •
0
Entering edit mode
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@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_ID ENTIFICATION=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_IDENTIFICATI ON=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 > > 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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLY •
0
Entering edit mode
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? Thank you very much! Yiwen -----Original Message----- From: Ben Bolstad [mailto:bmb@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_ID ENTIFICATION=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_IDENTIFICATI ON=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 > > 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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLY •
0
Entering edit mode
On Tue, Dec 23, 2008 at 1:02 PM, He, Yiwen (NIH/CIT) [C] < 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] > Sent: Tuesday, December 23, 2008 9:08 AM > To: balag Ganesan > Cc: He, Yiwen (NIH/CIT) [C]; 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> 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;L C_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_IDEN TIFICATION=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;L C_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 > > > 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 > > 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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
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_ID ENTIFICATION=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_IDENTIFICATI ON=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]]
ADD REPLY •
0
Entering edit mode
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_I DENTIFICATION=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_IDENTIFICAT ION=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 > >
ADD REPLY •
0
Entering edit mode
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@bmbolstad.com [mailto:bmb@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_I DENTIFICATION=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_IDENTIFICAT ION=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 > >
ADD REPLY •
0
Entering edit mode
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 >> >> > > >
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 428 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6