Identifying genes that contribute to limma's roast/romer gene set enrichments
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@gordon-smyth
Last seen 2 hours ago
WEHI, Melbourne, Australia
Dear Steve, The genes that contribute most to the roast result are the same genes that are ranked at the top in a standard genewise DE analysis, i.e., ranked by topTable(). Roast doesn't output the leading-edge genes because they are already available from the standard genewise analysis. The z-score is computed from the moderated t-statistics using zscoreT(). The roast help page says that the cutoff for PropDown and PropUp is z < -sqrt(2) and z > sqrt(2). The probability of this is: > 2*pnorm(-sqrt(2)) [1] 0.1572992 So the genes that contribute to PropUp and PropDown are those that have p-value less than 0.1572992 a standard genewise DE analysis. There is no exact equivalent for romer, but obviously looking at the genewise DE results will still reveal the most important genes. Best wishes Gordon > Stephen Hoang stephen.a.hoang at gmail.com > Fri Jan 31 21:58:26 CET 2014 > > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
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