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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 ATpoint ★ 2.8k
Applies to both.
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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Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Comment: Visualization of negative log CPM values
Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
Filtering low intensity probes in microarray data
Comment: Visualization of negative log CPM values
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