Bioconductor DiffSplice

Showing : diffSplice • reset

vote

replies

1.1k

views

diffSplice limma

3.4 years ago jamie.gearing ▴ 60

votes

replies

961

views

limma diffSplice

updated 4.3 years ago by Gordon Smyth 52k • written 4.3 years ago by gerberst • 0

vote

replies

1.6k

views

differential exon usage exon array analysis annotation hta2.0 diffsplice

updated 7.3 years ago by James W. MacDonald 67k • written 7.3 years ago by relathman ▴ 20

votes

replies

1.4k

views

limma diffSplice

updated 7.7 years ago by Gordon Smyth 52k • written 7.7 years ago by willj ▴ 30

votes

replies

3.7k

views

edgeR limma diffSplice DEXSeq

updated 8.4 years ago by Charity Law ▴ 90 • written 8.4 years ago by maltethodberg ▴ 180

votes

replies

1.3k

views

limma diffSplice plotSplice exons annotation

9.4 years ago Jose M Garcia Manteiga ▴ 310

6 results • Page 1 of 1

Recent ...

Replies

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 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…

Votes

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?

Awards • All