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Comment: Help with running egsea()
by
Chris
•
0
I tried egsea.ma and got this error:
gsa = egsea.ma(fit2, vector_group, probe_annotation, contrasts = contrast_matrix, gs.annots = gs.…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
•
0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
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: 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)`)?
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