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Comment: Warning message when running limma with covariates
by
Chris
▴
10
Hi Gordon,
My contract matrix has rows name: Intercept, vector_age, sex_vector2, group_vectorMCI. Column name design matrix: (Intercept), …
Answer: Warning message when running limma with covariates
by
Gordon Smyth
51k
The message seems self-explanatory, does it not? It is telling you that `row.names(contrast_matrix)` is not the same as `colnames(design)`.…
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…
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