How to do RMA without summary to probeset level?

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Peng Yu ▴ 940

@peng-yu-3586

Last seen 10.3 years ago

I use the following code to do RMA. I'm wondering how get the probe level values before the summary to the probeset level values. library(oligo) data<-read.celfiles(list.celfiles(data_dir, full.names=TRUE)) eset<-rma(data) write.exprs(eset, file='output_file_name', sep="\t")

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ADD COMMENT • link updated 15.0 years ago by Benilton Carvalho ★ 4.3k • written 15.0 years ago by Peng Yu ▴ 940

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Benilton Carvalho ★ 4.3k

@benilton-carvalho-1375

Last seen 4.8 years ago

Brazil/Campinas/UNICAMP

pm(data) b On Dec 26, 2009, at 2:21 PM, Peng Yu wrote: > I use the following code to do RMA. I'm wondering how get the probe > level values before the summary to the probeset level values. > > library(oligo) > data<-read.celfiles(list.celfiles(data_dir, full.names=TRUE)) > eset<-rma(data) > write.exprs(eset, file='output_file_name', sep="\t") > > _______________________________________________ > 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 COMMENT • link 15.0 years ago Benilton Carvalho ★ 4.3k

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library(oligo) data<-read.celfiles(list.celfiles(data_dir, full.names=TRUE)) pm(data) Do you mean the above commands? If that is the case, you misunderstood me. I don't need the original probe values. As far as I know, RMA does three things: background correction, quantile normalization, and summary from probes to probesets. I want the probe values after background correction and quantile normalization but before the summary. On Sat, Dec 26, 2009 at 12:07 PM, Benilton Carvalho <bcarvalh at="" jhsph.edu=""> wrote: > pm(data) > > b > > On Dec 26, 2009, at 2:21 PM, Peng Yu wrote: > >> I use the following code to do RMA. I'm wondering how get the probe >> level values before the summary to the probeset level values. >> >> library(oligo) >> data<-read.celfiles(list.celfiles(data_dir, full.names=TRUE)) >> eset<-rma(data) >> write.exprs(eset, file='output_file_name', sep="\t") >> >> _______________________________________________ >> 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 • link 15.0 years ago Peng Yu ▴ 940

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library(oligo) data = read.celfiles(list.celfiles(data_dir, full=T)) idx = oligo:::getFidProbeset(data) theProbes = exprs(data[idx,]) bgData = rma.background.correct(theProbes) normData = normalize.quantiles(log2(bgData)) On Dec 26, 2009, at 5:56 PM, Peng Yu wrote: > library(oligo) > data<-read.celfiles(list.celfiles(data_dir, full.names=TRUE)) > pm(data) > > Do you mean the above commands? If that is the case, you misunderstood > me. I don't need the original probe values. > > As far as I know, RMA does three things: background correction, > quantile normalization, and summary from probes to probesets. I want > the probe values after background correction and quantile > normalization but before the summary. > > On Sat, Dec 26, 2009 at 12:07 PM, Benilton Carvalho <bcarvalh at="" jhsph.edu=""> wrote: >> pm(data) >> >> b >> >> On Dec 26, 2009, at 2:21 PM, Peng Yu wrote: >> >>> I use the following code to do RMA. I'm wondering how get the probe >>> level values before the summary to the probeset level values. >>> >>> library(oligo) >>> data<-read.celfiles(list.celfiles(data_dir, full.names=TRUE)) >>> eset<-rma(data) >>> write.exprs(eset, file='output_file_name', sep="\t") >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > 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 • link 15.0 years ago Benilton Carvalho ★ 4.3k

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now that i think a bit more about this... if you want the control probes too, what i suggest is to use the following (yeah, yeah, it's not exposed): idx = oligo:::getFidProbeset(data) theProbes = exprs(data[idx,]) b On Dec 26, 2009, at 4:07 PM, Benilton Carvalho wrote: > pm(data) > > b > > On Dec 26, 2009, at 2:21 PM, Peng Yu wrote: > >> I use the following code to do RMA. I'm wondering how get the probe >> level values before the summary to the probeset level values. >> >> library(oligo) >> data<-read.celfiles(list.celfiles(data_dir, full.names=TRUE)) >> eset<-rma(data) >> write.exprs(eset, file='output_file_name', sep="\t") >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 • link 15.0 years ago Benilton Carvalho ★ 4.3k

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