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Answer: Filtering out non-variable probes from EPICv2 matrix
by
James W. MacDonald
68k
I wouldn't remove the CpGs. The idea behind DMR identification is to find regions with consistent changes in methylation, and if you select…
Answer: limma correction for tumor purity
by
James W. MacDonald
68k
The main purpose for `removeBatchEffect` is to adjust data for nuisance variables prior to plotting (a nuisance variable is meant to contro…
Comment: how to use `arrayWeightsQuick()`?
by
TraceMorrow
•
0
Yes, your proposed approach is correct. Using arrayWeightsQuick() after an initial lmFit() is suitable for large datasets, providing faster…
Comment: limma correction for tumor purity
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gabriella.jacobson-eisenberg
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0
I guess I'd like some further information of the use of covariate within limma for a continuous variable, when there is no batch being corr…
Comment: Gene Ontology (GO) Analysis
by
triyandornan
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0
Thank you so much for clarifying the difference!
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