> Date: Tue, 8 Sep 2009 12:28:28 -0400 > From: qq bioconductor <qq.bioconductor at="" gmail.com=""> > Subject: [BioC] Error when running limma on low variance data > To: bioconductor at stat.math.ethz.ch > Content-Type: text/plain > > Dear list member, > > I got an error message when running limma on my array dataset, which > contains a total of four Affy arrays from two different conditions. > > Error in if (evar > 0) { : missing value where TRUE/FALSE needed > In addition: Warning message: > In fitFDist(var, df1 = df) : > More than half of residual variances are exactly zero: eBayes unreliable > > I found the variances of most probesets in my dataset is 0. Therefore > median(fit$sigma^2) is 0. > The error is because in my case the "evar" variable in function fitFDist is > NaN, which is because some elements in the "e" variable are equal to -Inf > and "emean" is -Inf. > ( emean <- mean(e) > evar <- mean(n/(n - 1) * (e - emean)^2 - trigamma(df1/2)) > ) > > > Does anyone know how I can fix the error? Thank you! Yes. Stop trying to analyse data when all the residual variances are zero. It makes no sense to attempt a statistical analysis of such data, and it is a sure sign of an underlying problem with the data. At very least, you might filter out the probes with zero variances. Best wishes Gordon > Sincerely, > Qianqian