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Student
samples
sampleNumbers
DESeq2
written 2.2 years ago by
Lidia
• 0
6
votes
4
replies
1.6k
views
Which rlog should I use for DESeq2 analysis
samples
rlog
DESeq2
updated 2.6 years ago by
Michael Love
42k • written 2.6 years ago by
rafaelsolersanblas
▴ 50
0
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1
reply
667
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Paired samples in DESeq2
R
deseq2
Paired
Samples
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
m.wekking
• 0
2
votes
1
reply
895
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edgeR normalisation which samples to include
edger
normalization
samples
comparisons
updated 6.7 years ago by
Gordon Smyth
51k • written 6.7 years ago by
roser.navarro
• 0
4 results • Page
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Replies
Comment: Limma with covariates
by
Chris
▴ 10
Thank you James for the detailed follow up! I great appreciate it. The first model.matrix is similar to mine with 4 columns. Try your sugge…
Comment: Limma with covariates
by
James W. MacDonald
66k
There's a couple of things to unpack here. By default, if you specify no intercept (`~ 0 + ...`), then R will try to generate a cell means …
Comment: Limma with covariates
by
Chris
▴ 10
Thanks James! May I know why the sex covariate has two columns? Meanwhile, the groups also has 2 levels as sex but only has one column in t…
Answer: Limma with covariates
by
James W. MacDonald
66k
When you add the other coefficients to your model, you cannot have separate disease/control coefficients (unless you reorder and put diseas…
Answer: DESeq2 - vst() - log2FC - no replicates
by
ATpoint
★ 4.2k
You can subtract the vst values to approximate logFCs, see: https://support.bioconductor.org/p/106128/
Votes
Comment: Limma with covariates
A: Increase text size of axis labels in EnhancedVolcano
Answer: Limma with covariates
Answer: Limma with covariates
A: Combining ComplexHeatmap with other plot types
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