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hasaru-k / GlimmaV2

interactive plots for differential expression analysis
GNU Lesser General Public License v3.0
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Deseq2 no negative logCPM #76

Open Pahi95 opened 3 years ago

Pahi95 commented 3 years ago

Hi!

I really love your work! I'm doing a paralel analysis with deseq2 and edgeR, and when I plot the results, I don't get negative logCPM values for the Deseq dataset, but there should be, becouse if I do an individual table to check the cpm values, there are negative ones.

Can you please help? Thank you!

hasaru-k commented 1 year ago

Hey there! Sorry for the belated reply, and thanks so much!

Is the issue that DESeq2 isn't plotting negative logCPM values as expected? If so, I'd direct you to https://github.com/mikelove/DESeq2/issues/ as that's a different package :)