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TCGAWorkflow
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Identifying presence of certain genes
DifferentialExpression
TCGAWorkflow
2.5 years ago
Sam
▴ 10
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751
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tcga expression data
TCGAWorkflow
updated 20 months ago by
ATpoint
★ 4.1k • written 20 months ago by
fatemehfakhari74
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646
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Query on TCGA
TCGAbiolinks
TCGAWorkflow
20 months ago
hemangininaik09
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299
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Gene A mutation vs Gene B amplification using TCGA datasets
TCGAWorkflow
12 months ago
Begin-R
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Postdoc
TCGAWorkflow
3 months ago
sameerahmadguru
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Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
nbay13
• 0
A little late to the party, but I found that using the equation you specified, the p-values are actually slightly off from base R's `t.test…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
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