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Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
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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
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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…
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Gordon Smyth
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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
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James W. MacDonald
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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
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James W. MacDonald
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If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
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