User: drikaul

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drikaul0
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Posts by drikaul

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Comment: C: edgeR DE gene calculation problem
... that makes sense! But what if you were trying to tweak the number of columns (samples in the above example)? Working off of Jason's example, what if one were to subset the number of samples to just keep the "treatment" to see what DGE genes were up/down regulated in that particular subset, would you ...
written 2.2 years ago by drikaul0
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Answer: A: Differences in PCA plot - rld versus vsd normalized data (DESeq2)
... You could try removing the batch effects, limma has a function you could use for that (http://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/limma/html/removeBatchEffect.html). But from the plots, it seems like there's a distinction in the data already. Moreover, I would recommend using plo ...
written 2.2 years ago by drikaul0

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