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Answer: Right way to pseudobulk donors across replicates in edgeR
by
Reza Ghamsari
• 0
Hi Jack, Sorry if this is a naive question, but I'm a bit lost here. If I understand correctly, you have six batches (run) of 10x single…
Answer: limma comparison for small sample size and how to get covariance matrix
by
Gordon Smyth
51k
limma has already downweighted the outlier samples, which is the purpose of `sample.weights=TRUE` in the `voomLmFit()` call. So limma has a…
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…
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Comment: Limma with covariates
Answer: Limma with covariates
A: How to use GenomicRanges to find overlaps by percentage covered of interval
Comment: Limma with covariates
A: Increase text size of axis labels in EnhancedVolcano
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