User: adnbps

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adnbps10
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Posts by adnbps

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GSEA - Calculate the probability of each gene being enriched?
... I'm interested in constructing a gene module of genes that are co-expressed with gene A. To define this module, I calculate the correlation of gene A with all other genes, producing a vector of correlation coefficients: R = {ra, rb, rc, ...} I think this module should be enriched in a particular p ...
gene module gsea rna-seq statistics written 14 months ago by adnbps10 • updated 13 days ago by Biostar ♦♦ 20
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Comment: C: GO analysis: DAVID vs GREAT vs GOrilla
... I'm guessing they want the *full* gene list associated with each term. enrichr only shows the genes that are also in your gene set. ...
written 19 months ago by adnbps10
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Comment: C: Easy way to do GO enrichment in R
... enrichr was published in a good journal (NAR) and is not exactly a black box. While they provide a correction to the Fisher exact test, you don't have to use it. They also give you the uncorrected p-values. Of course, you should use whatever tool you prefer, but I don't want to give other people th ...
written 19 months ago by adnbps10
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Answer: A: Problem with topGO: GO term enrichment analysis
... The topGO documentation is impossible to follow. You might try using "enrichr" instead: http://amp.pharm.mssm.edu/Enrichr/ There is also an R version available. I got this up and running in a few minutes, versus fumbling around with topGO for hours. ...
written 19 months ago by adnbps10

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