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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Andre
•
0
I edited the previous post. I meant to remove the estimateGLMRobustDisp line in the second snipper :
````
DGE_list_object <- estimateGLMR…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Gordon Smyth
52k
Sorry, I had forgotten estimateGLMDisp() produces weights as well as NB dispersions. The weights from estimatGLMRobustDisp() were intended …
Answer: Mean variance curve troubleshoot filtering
by
Gordon Smyth
52k
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
You will get NA coefficients from `~Group+Batch` because the Group factor is completely confounded with the batch factor.
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)…
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