User: natalia.pietrosemoli

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Posts by natalia.pietrosemoli

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Comment: C: Camera gene set interpretation
... Thank you guys for the answers, took some time, but finally got it!   ...
written 9 months ago by natalia.pietrosemoli0
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Comment: C: Camera gene set interpretation
... If I''ve previously defined my design: > des   Mock_3h Z_3h 1       1    0 2       1    0 3       1    0 4       0    1 5       0    1 6       0    1 wouldn't this instruction: camera(exp.mat.0, indices, des, contrast=2) specifiy that I run my test for my condition Z_3h? this is how I interp ...
written 9 months ago by natalia.pietrosemoli0 • updated 9 months ago by Gordon Smyth32k
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Comment: A: Camera gene set interpretation
... I was just trying a shortcut to typing my whole code. Which is here. And it works, my question still remains the same. runTest <- function(iset,name, final.table, grp){   c(grep(grp[1], colnames(final.table),ignore.case = F ), grep(grp[2], colnames(final.table),ignore.case = F))->curr.ind   e ...
written 9 months ago by natalia.pietrosemoli0
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Camera gene set interpretation
... Dear all, After some careful reading, I've settled for CAMERA as my favaorite gene set enrichment test. However, in one of my datasets (condition 3 vs condition 1; 3 replicates, microarray data), I get a very confusing error: I get  virtually the  same enriched gene sets (and direction!) when I p ...
limma camera gene set analysis gene set enrichment written 9 months ago by natalia.pietrosemoli0 • updated 9 months ago by Gordon Smyth32k
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Comment: C: using camera/roast/romer to find enriched gene sets from proteomics data
... Dear Gordon, Thanks so much for your quick response. In fact, you are right. I tried voom and then I realised it was not apprapriate, so I'm not using it anymore, but I did this part of the anlysis long ago, and had forgotten about it. I was in distress becuase I had a moment of 'phylosophical' do ...
written 13 months ago by natalia.pietrosemoli0
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using camera/roast/romer to find enriched gene sets from proteomics data
... Dear all,   I'm perfoming a proteomics analysis (using limma-voom) to get differentially expressed proteins among several conditions. Could I also benefit from the gene set tests in the limma package as well (provided that I make the necessary adjustments from proteins to gene ids?)   Thanks a  ...
proteomics limma camera mroast romer written 13 months ago by natalia.pietrosemoli0 • updated 13 months ago by Gordon Smyth32k

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