Ok thanks. On 01/17/2011 02:25 PM, Sean Davis wrote: > On Mon, Jan 17, 2011 at 8:09 AM, David martin<vilanew at="" gmail.com=""> wrote: > >> Hello, >> I'm having problems computing comparisons between different groups (this is >> not array data and i'm not using limma). Any on what the error must be ? >> >>> mydata.eset >> ExpressionSet (storageMode: lockedEnvironment) >> assayData: 2754598 features, 3 samples >> element names: exprs >> protocolData: none >> phenoData >> sampleNames: sampleA sampleB sampleC >> varLabels: Group Sample >> varMetadata: labelDescription >> featureData: none >> experimentData: use 'experimentData(object)' >> Annotation: >> >> >> fit<- lmFit(mydata.eset, design) >> .... >> contrast.matrix >>> contrast.matrix >> group1-group2 >> group1 1 >> group2 -1 >> group3 0 >> group1-group3 >> group1 1 >> group2 0 >> group3 -1 >> group2-group3 >> group1 0 >> group2 1 >> group3 -1 >> >> fit2<- contrasts.fit(fit, contrast.matrix) >> fit2<- eBayes(fit2) >> Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = >> stdev.coef.lim) : >> No residual degrees of freedom in linear model fits >> >> > Hi, David. > > You have three samples and three conditions. That is not enough samples to > perform the tests that you want to perform. Your only recourse here, > really, is to make ratios among your three arrays and rank genes based on > fold change. Alternatively, you can go run some biological replicates. > > Sean > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >