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Answer: DESeq2 or edgeR for Presence and Absence of Proteins
by
ATpoint
★
2.8k
No, both tools expect count data with certain distributional assumptions which are not satisfied by binary data.
Since you're a master …
Comment: Visualization of negative log CPM values
by
Gordon Smyth
47k
Sorry, but some of the things you say are not correct.
> compound B has 2 statistically significant genes that are up-regulated
No, there…
Comment: Visualization of negative log CPM values
by
Sabiha
▴
10
@atpoint OK, are you referring to the `log2(cpm+1)` or `log2(tpm+1)`
Comment: Visualization of negative log CPM values
by
Sabiha
▴
10
@gordonsmyth noted. Related to the graphs above, the table below is the output from `limma`, and compound B has 2 statistically significant…
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