User: Xavier

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Xavier10
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9 months, 3 weeks ago
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10 months ago
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Posts by Xavier

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Answer: A: GOseq package: Which genes are included in the "numDEInCat"?
... I know see, everything seems to work now. Again, thank you so much for your help!  ...
written 10 months ago by Xavier10
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Answer: A: GOseq package: Which genes are included in the "numDEInCat"?
... # Thanks, commend #5 now works: allKEGG_sig <- allKEGGs[allKEGGs$values %in% KEGG.sig$category,] # However, the last command does not work: allKEGG_sig2 <- allKEGG_sig[allKEGG_sig$ind %in% sig_genes,] # It gives the following error: > allKEGG_sig2 <- allKEGG_sig[allKEGG_sig$ind %in% si ...
written 10 months ago by Xavier10
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Comment: C: GOseq package: Which genes are included in the "numDEInCat"?
... # This was the "original" code: kegg <- lapply(en2eg, grepKEGG, eg2kegg) KEGG=goseq(pwf, gene2cat=kegg) KEGG.sig <- KEGG[KEGG$over_represented_pvalue<0.05,] # This is the code adjusted based on your input: kegg <- lapply(en2eg, grepKEGG, eg2kegg) KEGG=goseq(pwf, gene2cat=kegg) allKEGGs ...
written 10 months ago by Xavier10
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Answer: A: GOseq package: Which genes are included in the "numDEInCat"?
... Unfortunately this doesn't work. The 5th command ( "allKEGG_sig <- allKEGGs[allKEGGs$values %in% enriched.kegg,]") does not work as it gives no data. Any other solutions? ...
written 10 months ago by Xavier10
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GOseq package: Which genes are included in the "numDEInCat"?
... Hi, I've performed KEGG pathway analyses using the GOseq package and now I was wondering how do I know which genes were included in the "numDEInCat"? See below for example:  Category Over_represented_pvalue Under_represented_pvalue numDEInCat numInCat pathway 01100 ...
goseq kegg written 10 months ago by Xavier10

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