Dear Amit, Apparently the sampleNames are not the same in your assayData and in your phenoData, you should carefully check this first. The expressionSet should contain the M values. For the conversion, you can try: new("ExpressionSet",exprs=rat_norm_MA$M) Best wishes, Audrey -- Audrey Kauffmann Bergonie Cancer Institute 229 Cours de l'Argonne 33076 Bordeaux France +33.5.56.33.04.53 2010/4/15 Amit <amitkumartiwary@gmail.com> > Dear Wolfgang, > > Thank you for your reply. I asked that question because > arrayQualityMetrics gives following error with MAList object: > #loading required libraries > >library(convert) > >library(arrayQualityMetrics) > #loading MAList object into R > > load("rat_norm_MA.RData") > > dim(rat_norm_MA$M) > [1] 20500 363 > > dim(rat_norm_MA$A) > [1] 20500 363 > > qm=arrayQualityMetrics(rat_norm_MA,"qm_rat") > Error in validObject(.Object) : > invalid class "ExpressionSet" object: sampleNames differ between > assayData and phenoData > Error in arrayQualityMetrics(rat_norm_MA, "qm_rat") : > The expressionset is a MAList and cannot be converted automatically > in a ExpressionSet. Try to convert it manually. > > Hence, I wish to know if arrayQualityMetrics works on M or A, so that > I could convert one of these to ExpressionSet and run > arrayQualityMetrics on it. > > Best! > Amit > > On Thu, Apr 15, 2010 at 12:02 AM, Wolfgang Huber <whuber@embl.de> wrote: > > Dear Amit > > > > have a look at the manual page of the 'arrayQualityMetrics' function. > There, > > you can see that it accepts 'MAList' objects directly, and extracts the > > needed information from that. > > > > Another way to learn more about this package is its vignette, which you > can > > view with > > vignette("arrayQualityMetrics") > > > > Best wishes > > Wolfgang > > > > > >> Dear All, > >> > >> I am working on large dataset of two color arrays. For two color > >> arrays the normalizeBetweenArray function (limma) produces MAList from > >> RGList after normalization. My question is after normalization of two > >> color microarray data, whether arrayQualityMetrics should be run on M > >> (log ratios) matrix or A (average log intensity) matrix ? I am > >> guessing it should be run on A matrix as arrayQualityMetrics requires > >> matrix of microarray intensities to perform the analysis. But, I am > >> not sure. Any suggestion is appreciated. > >> > >> regards > >> Amit > >> > >> _______________________________________________ > >> 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 > > > > -- > > > > > > Wolfgang Huber > > EMBL > > http://www.embl.de/research/units/genome_biology/huber > > > > > > > > _______________________________________________ > 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]]