Identifying genes that contribute to limma's roast/romer gene set enrichments
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@stephen-hoang-6156
Last seen 6.3 years ago
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 in the output of roast? And is the analogous gene set knowable in the case of romer? I see in roast help page that the "up" and "down" genes are categorized as such based on a z-score threshold, but what are the values in this distribution -- global fold changes, fold changes within a gene set, or something else altogether? Thanks in advance, Steve [[alternative HTML version deleted]]
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