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How to get multi-factor Deseq LRT test log P values for a particular condition
Deseq2
LRT
Factors
RNAseq
3.7 years ago
aishu.jp
▴ 30
2
votes
3
replies
525
views
RNA seq with edgeR with several factors
RNAseq
factors
12 months ago
Nathalie
▴ 20
0
votes
3
replies
837
views
I have a problem when I run DESeq2 with one variable with 8 levels, I can't find the contrast for any comparison with level 8
Contrast
factors
levels
18 months ago
Edgar
• 0
1
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1
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836
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Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Alex
• 0
4 results • Page
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Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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