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Design
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Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 1 day ago by
swbarnes2
★ 1.3k • written 2 days ago by
arfranco
▴ 130
3
votes
6
replies
842
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
2
votes
3
replies
293
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
JKim
• 0
2
votes
2
replies
290
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
12 weeks ago
SamGG
▴ 350
2
votes
2
replies
262
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
7 weeks ago
Sabiha
▴ 20
5 results • Page
1 of 1
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Replies
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons
by
Michael Love
41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
Comment: Too many significant genes when integrating gtex and tcga
by
ATpoint
★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Votes
Print Differentially Expressed Exons From Dexseq Results
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
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