Hence, DESeq2 offers two possible responses to flagged outliers. By default, outliers in conditions with six or fewer replicates cause the whole gene to be flagged and removed from subsequent analysis, including P value adjustment for multiple testing. For conditions that contain seven or more replicates, DESeq2 replaces the outlier counts with an imputed value, namely the trimmed mean over all samples, scaled by the size factor, and then re-estimates the dispersion, LFCs and P values for these genes. As the outlier is replaced with the value predicted by the null hypothesis of no differential expression, this is a more conservative choice than simply omitting the outlier. When there are many degrees of freedom, the second approach avoids discarding genes that might contain true differential expression.
