Unless I'm much mistaken, CuffDiff pools reads from all samples within a condition prior to differential expression analysis. Does anyone understand the method by which CuffDiff prevents an outlier (for instance, one sample overexpressing a gene significantly more than the others) from skewing the results? How reliable have other users found this method to be?
(I did read http://cufflinks.cbcb.umd.edu/howitworks - just having some difficulty understanding it).
(I did read http://cufflinks.cbcb.umd.edu/howitworks - just having some difficulty understanding it).
Comment