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deseq2 sample check is failingi #126

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slsevilla opened this issue Mar 4, 2024 · 1 comment · Fixed by #127
Closed

deseq2 sample check is failingi #126

slsevilla opened this issue Mar 4, 2024 · 1 comment · Fixed by #127
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@slsevilla
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slsevilla commented Mar 4, 2024 •
edited by kelly-sovacool
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From Erica

hi Sam, good morning! I'm still running into some DESeq2 issues with CARLISLE that I wanted to run by you. All of my conditions have at least 3-4 replicates, but (Sh2 vs PC) are failing during the check for single-sample groups, while the other half (Sh1 vs PC) are being treated as having a single sample and producing empty output files. I think this might be because they have a "1" in the group name. I'm going to comment out the check for my projects, but just wanted to let you know!

Will need to design a better way to determine samples vs groups
@slsevilla slsevilla self-assigned this Mar 4, 2024
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_diff_markdown_wrapper.R, line 90 - log2FC is being assigned FDR cutoff

@epehrsson epehrsson mentioned this issue Apr 11, 2024
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