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Comment: Package needs internet access
by
James W. MacDonald
67k
It's not clear to me why (or that) `seqlevelsStyle` should be called on a `BSgenome` object. You will need to provide more code that preced…
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
by
James W. MacDonald
67k
The 'voom transformed counts' are just logCPM with a prior count of 0.5. The 'magic' of limma-voom is the weights that are computed and the…
Answer: Limma Interaction Effect with Covariates
by
James W. MacDonald
67k
The second way is how you should do it.
Answer: Using Affymetrix Custom Array
by
James W. MacDonald
67k
To use `gcrma` you need to have the probe sequences for that array. It doesn't appear that ArrayExpress has the probe sequences, and I don'…
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