User: Stephen Hoang

gravatar for Stephen Hoang
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1 year, 10 months ago
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Posts by Stephen Hoang

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Comment: C: Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
... To follow up, is it reasonable to use the QL pipeline with the estimateGLMRobustDisp? Thanks. ...
written 23 months ago by Stephen Hoang30
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Random effects with limma's camera()
... Hi All, Is there a way to incorporate the consensus correlation calculated by duplicateCorrelation() into the gene set enrichment test performed by camera()? In short, I would like to treat one of my factors as a random effect via duplicateCorrelation() (this is what I did for differential expressi ...
limma camera duplicatecorrelation written 3.7 years ago by Stephen Hoang30 • updated 3.7 years ago by Gordon Smyth39k
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Identifying genes that contribute to limma's roast/romer gene set enrichments
... Hi All, Is there a way to identify the genes that contribute to the gene set enrichments calculated by roast/romer? I realize that all of the genes in a given set are contributing to the p-value calculation, but is there a way to get at, for example, the genes that contribute to the "PropUp" value ...
written 5.8 years ago by Stephen Hoang30
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Comment: C: unexpected voom! / limma contrast inconsistency
... Dear Gordon, Thank you very much for the helpful clarification. In the case that a blocking variable is given to lmFit (in my case, to specify duplicate correlation), along with a design of the form model.matrix(~0+a), will contrasts.fit() produce approximate or exact results? Intuitively, it seem ...
written 6.1 years ago by Stephen Hoang30 • updated 4.0 years ago by Gordon Smyth39k
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unexpected voom! / limma contrast inconsistency
... Hi All, We have come across somewhat unexpected behavior from voom! / limma that is worth sharing. We found that using the same data, but different design matrices, "equivalent" contrasts can yield different results. We constructed a design matrix, such that to make our desired contrast (treatment ...
limma written 6.2 years ago by Stephen Hoang30 • updated 4.0 years ago by Gordon Smyth39k

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Popular Question 23 months ago, created a question with more than 1,000 views. For unexpected voom! / limma contrast inconsistency

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