Hi Jane On 08/08/2011 02:45 PM, Wolfgang Huber wrote:
in the case of genes (or better term: loci) with only one exon, DEXSeq's testGeneForDEU does not make sense - it is looking for exons within the locus that behave differently from the average of all the others: there are no others! Hence the parameters are unidentifiable, and the software should not even look at them.
Actually, it doesn't. This is why the p value is NA. Also note the column 'testable' in the fData data frame: it is set to FALSE in such cases to indicate that a test was not attempted. You will also find testable=FALSE occasionally in genes with more than one exons, namely whenever all exons or all exons but one have zero counts in all samples.
Cheers Simon _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
