Hi I wanted to calculate coefficients of variation for some genes using data analysed with limma (two-colour microarray data), and found that the SD for all genes in each comparison were the same e.g. from fit$stdev.unscaled Comparsion 1 Comparison 2 Comparison 3 Min. :0.5599 Min. :0.5599 Min. :0.7919 1st Qu.:0.5599 1st Qu.:0.5599 1st Qu.:0.7919 Median :0.5599 Median :0.5599 Median :0.7919 Mean :0.5599 Mean :0.5599 Mean :0.7919 3rd Qu.:0.5599 3rd Qu.:0.5599 3rd Qu.:0.7919 Max. :0.5599 Max. :0.5599 Max. :0.7919 I understand that eBayes uses a pooled variance approach but these values are obtained before eBayes was used. Could anyone help explain the values I am getting please ? Cheers Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919