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Answer: how to understand cpm=1 and how filterByExpr works?
by
gowthamee
•
0
I found the following two articles very helpful in explaining the functions "cpm" and "filterByExpr"
Article#1: From reads to genes to pat…
Comment: different results in DESeq2 when comparing groups in two ways
by
zohreh.fazelan
•
0
Thank you for your response.
But I have few comparisons in which there are more significantly expressed genes in the socond way compared to…
Comment: lmFit, continuous exposure, adjustment covariates
by
Gordon Smyth
45k
Your code `t(dat[43:ncol(dat)]` is not even syntactically correct. It could not possibly run in R.
You need to create an expression matrix…
Comment: Handling of missing values in limma
by
Gordon Smyth
45k
limma uses all the observations. There's nothing complicated about it.
limma does not remove any persons from the analysis.
I did not tel…
Answer: after calcNormFactors with EdgeR, how to get TMM normalized matrix?
by
Gordon Smyth
45k
There's no such thing as a "TMM normalized matrix" or "normalized values" in edgeR. Have you read the edgeR User's Guide for how analyses a…
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