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Answer: Reproducibility using limma for DE Analysis
by
TSauer
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Yes, i know that. However, I implemented the imputation step quite long ago, using a different package, exported the data and then did the …
Comment: Reproducibility using limma for DE Analysis
by
Gordon Smyth
47k
limma can also be run without imputation, i.e., leaving the missing values as NA.
Comment: Reproducibility using limma for DE Analysis
by
TSauer
•
0
Hey Gordon,
thank you for the swift response.
Indeed, I do perform imputation. Weirdly, it did not occur to me that this could be the origi…
Answer: Reproducibility using limma for DE Analysis
by
Gordon Smyth
47k
limma has no random component and limma analyses are completely reproducible. limma doesn't have any dependence on the random number seed.
…
Comment: In WGCNA which is the matrix on which the eigen decomposition is run to get the
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andres.firrincieli
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50
cross-posted on r/bioinformatic:[link][1]
To calculate the module eigengenes with `moduleEigengenes()` will need the normalized expression…
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