R: DESeq2 analysis: outliers and refitting
When I was running DESeq2, I got the message shown as below: converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing -- replacing outliers and refitting for 47 genes -- DESeq argument 'minReplicatesForReplace' = 7 -- original counts are preserved in counts(dds) estimating dispersions fitting model and testing I didn't encounter this before. Here are the reasons: Answers: The count outlier flagging is useful when there are a minority of outliers in the dataset, but as you have noted, something else is going on here with so many genes flagged. There are two reasons for so many genes being flagged as outlier: either the method for flagging outliers is not appropriate for the distribution of counts in your data and should be turned off (by setting minReplicatesForReplace=Inf and cooksCutoff=FALSE), or you have a sample...