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Answer: Normalized counts from LRT or Wald test?
by
ATpoint
★
2.8k
If the same samples are present in the object then the normalized counts are exactly the same independent of the design or test you use.
Comment: Visualization of negative log CPM values
by
Gordon Smyth
47k
Sorry, I was wrong to say that log2(TPM) is always negative, but log2(TPM) is not more likely that log2(CPM) to be positive if both are com…
Comment: Visualization of negative log CPM values
by
Sabiha
▴
10
@gordonsmyth Apologies, I used a wrong term, I would have mentioned raw `p-value` instead. Unfortunately, only 3 gene passed FDR (BH) in th…
Comment: Extracting fitted expression matrix from Limma
by
sarah.kelliher
•
0
Thank you Prof Smyth for your prompt and informative reply, much appreciated.
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 …
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