I am running DESeq2_1.10.1 on a data set with a continuous predictor term (either with or without a categorical blocking term).
My understanding is that in such cases, outlier detection and replacement is not automatically applied, and instead it's necessary to conduct a manual inspection of Cook's distances. I base this on section 3.6 of the Nov 30 2016 version of the DESeq2 vignette www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf)
However, when I run the DESeq function, I see the following message:
- fitting model and testing
- -- replacing outliers and refitting for 361 genes
- -- DESeq argument 'minReplicatesForReplace' = 7
- -- original counts are preserved in counts(dds)
My question, then, is what actually is happening here? Am I looking at a copy of the vignette that is out of date? Is my analysis carrying out the outlier replacement procedure even though it's not optimal for continuous predictors? Or am I misinterpreting the message entirely?
Thank you in advance! I can provide more details about my DESeqDataSet object if helpful.