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! Sincerely, Qianqian [[alternative HTML version deleted]]

Hi, Qianqian, As Gordan mentioned, you can try to filter out probes that are lack of variation by using 'nsFilter' or 'varFilter' functions in the genefilter package. Hope this would help. Chao-Jen qq bioconductor wrote: > 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! > > Sincerely, > Qianqian > > [[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 > -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M2-B876 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org