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factors
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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
1
vote
1
reply
840
views
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
2
votes
3
replies
525
views
RNA seq with edgeR with several factors
RNAseq
factors
12 months ago
Nathalie
▴ 20
0
votes
3
replies
841
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
4 results • Page
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Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark?
by
Juan Higareda
• 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance
by
James W. MacDonald
65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip
by
James W. MacDonald
65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
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Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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