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Comment: deseq2 filter the low counts
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> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
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Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something?
I have 6 treatments, …
Comment: deseq2 filter the low counts
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Michael Love
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Have you seen this part:
https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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empty_mt
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Hi Michael,
My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
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That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files.
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