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The commands eset <- rma(Data) and eset <- expresso(Data, bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly",summary.method="medianpolish") should (in theory) be giving the same expression values. While the example you mention does appear in the main affy vignette I am not sure that it is ever presented as being the way to compute RMA expression values using the expresso function. Best, Ben On Mon, 2007-09-10 at 10:00 +1000, Yogi Sundaravadanam wrote: > Hello all > > > > I am pretty new to using Bioconductor packages and R software, and I was > wondering if you could help please? > > > > Whats the difference between the following please? > > > > eset <- rma(Data) > > and > > eset <- expresso(Data, normalize.method="qspline", > bgcorrect.method="rma", > > pmcorrect.method="pmonly", > summary.method="liwong") > > > > > > if rma does background corrections, normalises using quantile > normalisation, and calculates expresssion measure using median polish > (assuming that is what rma does), are the above two commands just the > same? > > > > Also, in the Affy package documentation, is the following line an > errata? > > eset <- expresso(affybatch, normalize.method="qspline", > bg.method="rma",pmcorrect.method="pmonly",summary.method="liwong" > > I cant seem to find documentation for bg.method? > > > > Thanks heaps > > Yogi > > > > _____ > > Yoganand Sundaravadanam > Bioinformatics Officer > > Australian Genome Research Facility Ltd > Email: yogi.sundaravadanam at agrf.org.au > Web: www.agrf.org.au > Subscribe to the AGRF Newsletter > > _____ > > Please Note: The message is intended only for the addressee. If you > receive this message in error please do not publish, distribute, or copy > it. Please advise the AGRF by telephone or email, and delete this > message from your computer. > > > > > > [[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