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BioInfoBeginnerrr
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Answer: batch effect correction before DESeq2 analysis
by
ATpoint
★
2.1k
This is covered in the vignette. Including batch into the design is recommending for DE testing and removal from transformed counts is reco…
Answer: Reproducibility using limma for DE Analysis
by
TSauer
•
0
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.
…
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