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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Gordon Smyth
52k
Sorry, I cannot follow what you're saying. The two code sequences you show look to be exactly the same.
Answer: Mean variance curve troubleshoot filtering
by
Gordon Smyth
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You could use `filterByExpr()`, as recommended by Law et al (2018) and in the limma and edgeR case studies.
However, the main problem wi…
Comment: How do I fix an odd voom plot in a combined dataset?
by
Gordon Smyth
52k
The fact that you have partial NA coefficients indicates that your merged dataset consists in good part of NAs for a very large number of g…
Comment: How do I fix an odd voom plot in a combined dataset?
by
1sunmic2
•
0
Thanks for responding! I did change the code slightly:
dge1 <- DGEList(counts = combined_data_counts)
keep <- rowSums(cpm(dge1)…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Andre
•
0
The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1).
If I use estimateGLMRobustDisp(), like…
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