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contrasts
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3
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
bioinf
▴ 10
2
votes
3
replies
292
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
0
votes
3
replies
661
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 9 months ago by
James W. MacDonald
65k • written 10 months ago by
a26fd14e
• 0
1
vote
2
replies
563
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
10 months ago
jovel_juan
▴ 30
4 results • Page
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
by
James W. MacDonald
65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Votes
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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