updated 8.1 years ago by
Gordon Smyth
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written 8.1 years ago by
Pekka Kohonen
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Comment: deseq2 filter the low counts
by
Michael Love
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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)…
Comment: deseq2 filter the low counts
by
empty_mt
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0
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
by
Michael Love
43k
Have you seen this part:
https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts
by
empty_mt
•
0
Hi Michael,
My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
•
0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files.
I'm able to read in the file…
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