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12 results • Page 1 of 1

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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

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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Answer: How do I fix an odd voom plot in a combined dataset?

Comment: How do I fix an odd voom plot in a combined dataset?

C: How does edgeR cpm function calculate log(CPM) values?

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