subtractmm problem in "affy"
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@parkchristopher-changsun-723
Last seen 10.2 years ago
Hi all, I am trying to normalize microarray data using the subtractmm method using the "affy" library. The following is my R script: set.seed(123) library(affy) Data <- ReadAffy() eset<-expresso(Data,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="subtractmm", summary.method="medianpolish") write.exprs(eset,file="subtractmm_data.txt") During the normalization, I encounter the following error message: Error in if (converged) break : missing value where TRUE/FALSE needed In addition: Warning message: NaNs produced in: log(x, base) ... The processed data is a grid of NA's. Does anyone know what might be wrong here and what I could do to fix it? Thanks again for your help, Chris
Microarray Normalization Microarray Normalization • 1.2k views
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Ben Bolstad ★ 1.1k
@ben-bolstad-93
Last seen 10.2 years ago
the problem is that the medianpolish summarization method takes a log2 transformation of the data. if you use subtractmm there is the possibility of gettting negatives. Perhaps you want to use pmcorrect.method="mas" which will used a modified version of MM. This will not give you the same problem of NA. On Wed, 2004-04-21 at 13:49, PARK,CHRISTOPHER CHANGSUN wrote: > Hi all, > > I am trying to normalize microarray data using the subtractmm method using > the "affy" library. > > The following is my R script: > > set.seed(123) > library(affy) > Data <- ReadAffy() > eset<-expresso(Data,bgcorrect.method="rma", > normalize.method="quantiles", > pmcorrect.method="subtractmm", > summary.method="medianpolish") > write.exprs(eset,file="subtractmm_data.txt") > > During the normalization, I encounter the following error message: > > Error in if (converged) break : missing value where TRUE/FALSE needed > In addition: Warning message: > NaNs produced in: log(x, base) > ... > > The processed data is a grid of NA's. > > Does anyone know what might be wrong here and what I could do to fix it? > > Thanks again for your help, > Chris > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad
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@anja-von-heydebreck-625
Last seen 10.2 years ago
I'm wondering whether a problem with Ben's suggestion might be that in expresso, the pmcorrect step is applied after background correction (and normalization), and the RMA bg correction is applied to the PM intensities only. So, as far as I understand, by choosing pmcorrect.method other than "pmonly" together with "bgcorrect.method="rma", one would subtract not-bgcorrected MM intensities from bgcorrected PM intensities. > Date: Wed, 21 Apr 2004 13:55:12 -0700 > From: Ben Bolstad <bolstad@stat.berkeley.edu> > Subject: Re: [BioC] subtractmm problem in "affy" > To: "PARK,CHRISTOPHER CHANGSUN" <ccpark@ucla.edu> > Cc: bioconductor@stat.math.ethz.ch > Message-ID: <1082580912.1635.56.camel@bmbbox.dyndns.org> > Content-Type: text/plain > > the problem is that the medianpolish summarization method takes a log2 > transformation of the data. if you use subtractmm there is the > possibility of gettting negatives. Perhaps you want to use > > pmcorrect.method="mas" > > which will used a modified version of MM. This will not give you the > same problem of NA. > > > On Wed, 2004-04-21 at 13:49, PARK,CHRISTOPHER CHANGSUN wrote: > > Hi all, > > > > I am trying to normalize microarray data using the subtractmm method using > > the "affy" library. > > > > The following is my R script: > > > > set.seed(123) > > library(affy) > > Data <- ReadAffy() > > eset<-expresso(Data,bgcorrect.method="rma", > > normalize.method="quantiles", > > pmcorrect.method="subtractmm", > > summary.method="medianpolish") > > write.exprs(eset,file="subtractmm_data.txt") > > > > During the normalization, I encounter the following error message: > > > > Error in if (converged) break : missing value where TRUE/FALSE needed > > In addition: Warning message: > > NaNs produced in: log(x, base) > > ... > > > > The processed data is a grid of NA's. > > Best, Anja -- Dr. Anja von Heydebreck Department of Bio- and Chemoinformatics Merck KGaA 64271 Darmstadt, Germany Phone: ++49-6151-723235 Fax: ++49-6151-723329 anja.von.heydebreck@merck.de
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Yes you are correct. if you read the "affy: built in processing methods" vignette, it is clearly spelled out in section 6 that "It is important to note that not every preprocessing method can be combined together. In particular the rma backgrounds adjust only PM probe intensities and so they should only be used in conjunction with the pmonly PM correction." It would be trivial for someone to modify their local bg.correct.rma to handle MM probes. Say something like: bg.correct.rma <- function(object, ...){ pm(object) <- apply(pm(object),2,bg.adjust) mm(object) <- apply(mm(object),2,bg.adjust) return(object) } or you could use bgcorrect.method="none" in the expresso() call On Thu, 2004-04-22 at 02:40, Anja von Heydebreck wrote: > I'm wondering whether a problem with Ben's suggestion might be that in > expresso, the pmcorrect step is applied after background correction (and > normalization), and the RMA bg correction is applied to the PM > intensities only. So, as far as I understand, by choosing pmcorrect.method > other than "pmonly" together with "bgcorrect.method="rma", one would > subtract not-bgcorrected MM intensities from bgcorrected PM intensities. > > > Date: Wed, 21 Apr 2004 13:55:12 -0700 > > From: Ben Bolstad <bolstad@stat.berkeley.edu> > > Subject: Re: [BioC] subtractmm problem in "affy" > > To: "PARK,CHRISTOPHER CHANGSUN" <ccpark@ucla.edu> > > Cc: bioconductor@stat.math.ethz.ch > > Message-ID: <1082580912.1635.56.camel@bmbbox.dyndns.org> > > Content-Type: text/plain > > > > the problem is that the medianpolish summarization method takes a log2 > > transformation of the data. if you use subtractmm there is the > > possibility of gettting negatives. Perhaps you want to use > > > > pmcorrect.method="mas" > > > > which will used a modified version of MM. This will not give you the > > same problem of NA. > > > > > > On Wed, 2004-04-21 at 13:49, PARK,CHRISTOPHER CHANGSUN wrote: > > > Hi all, > > > > > > I am trying to normalize microarray data using the subtractmm method using > > > the "affy" library. > > > > > > The following is my R script: > > > > > > set.seed(123) > > > library(affy) > > > Data <- ReadAffy() > > > eset<-expresso(Data,bgcorrect.method="rma", > > > normalize.method="quantiles", > > > pmcorrect.method="subtractmm", > > > summary.method="medianpolish") > > > write.exprs(eset,file="subtractmm_data.txt") > > > > > > During the normalization, I encounter the following error message: > > > > > > Error in if (converged) break : missing value where TRUE/FALSE needed > > > In addition: Warning message: > > > NaNs produced in: log(x, base) > > > ... > > > > > > The processed data is a grid of NA's. > > > > > Best, > Anja > > -- > Dr. Anja von Heydebreck > Department of Bio- and Chemoinformatics > Merck KGaA > 64271 Darmstadt, Germany > Phone: ++49-6151-723235 > Fax: ++49-6151-723329 > anja.von.heydebreck@merck.de > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad
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