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User: ahmed.asadik

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Posts by ahmed.asadik

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Retrieving corrected matrix after linear model adjustment
... Dear All, I am using the limma package for differential expression analysis. In my datasets there are strong confounding effects due to both technical variation and biological contamination of the tumor cells with infiltrating cells and stroma. I would like to cluster my patient samples after remo ...
limma sva written 17 months ago by ahmed.asadik0 • updated 17 months ago by James W. MacDonald49k
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Comment: C: Discrepancy in the output of decideTests (total not equal to sum of up/down gene
... Dear Gordon and Aaron, Thank you very much for your replies. This seems to solve the issue, but I have another question. Which genes should I use to run GSEA. Should I use the genes after the option include="both", or include=c("up", "down")? because the total number of genes from both options are ...
written 2.3 years ago by ahmed.asadik0
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Discrepancy in the output of decideTests (total not equal to sum of up/down genes)
... Dear All, I am having some strange experience with the function decideTests. When I compare between the total number of genes between my three groups and the the sum of the corresponding up and down genes the results are different. The sum is either larger than or smaller than the total. Am I doi ...
limma decidetests written 2.3 years ago by ahmed.asadik0 • updated 2.3 years ago by Gordon Smyth36k

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