Hi, Thanks in advance for any help. I have the latest R software (2.13.1) and edgeR software (2.8.4). I'm running into a problem where I estimate a common dispersion parameter of 0.0001 and when I subsequently estimate tagwise dispersions using the default prior.n = 10, the summary statistics are
Min. 1st Qu. Median Mean 3rd Qu. Max. 0.001 0.001 0.001 0.001 0.001 0.022 ie, all estimates are 10 times larger than the common dispersion estimate. Since the method is supposed to shrink toward the common value this seems a little surprising. When I increase prior.n to a large number I expect the tagwise estimates to all converge to the common dispersion, but as you might guess from the table above it converges to 0.001 = 10*common. The data comes from the bioconductor package "yeastRNASeq" and it appears from the description of the data that the two samples in each group are actually from sequencing the same extraction of mRNA, ie not biological and not even really technical replicates. So the common dispersion should be zero as the counts should follow the poisson. I cannot explain the behavior of the estimates but I'm afraid it might be something in the code so I'll include that below. library(yeastRNASeq) data( geneLevelData ) d <- DGEList( geneLevelData , group = c( rep( "Mutant" , 2 ) , rep( "Wild" , 2 ) ) ) d <- calcNormFactors( d ) d <- d[rowSums(d$counts) >= 5, ] d <- estimateCommonDisp( d ) d$common.dispersion [1] 0.000101 d <- estimateTagwiseDisp( d , prior.n = 10 ) summary( d$tagwise.dispersion ) Min. 1st Qu. Median Mean 3rd Qu. Max. 0.001 0.001 0.001 0.001 0.001 0.022 d <- estimateTagwiseDisp( d , prior.n = 1000 ) summary( d$tagwise.dispersion ) Min. 1st Qu. Median Mean 3rd Qu. Max. 0.001 0.001 0.001 0.001 0.001 0.001 It could just be an oddity of the data set itself but I don't have enough experience using edgeR across different RNA-Seq experiments to know how these methods should behave. Thanks, Sean [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing