User: thomasjenner333
thomasjenner333 • 0
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Posts by thomasjenner333
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... Hi Yu!
Yes, I had used the wrong file. Then I got the ones for Sus scrofa, and did the MSigdb gene set analysis. Thanks for pointing out the mistake.
The answer that I've posted, is that an acceptable approach to get a list of pathways? Thanks for your help.
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written 6 months ago by
thomasjenner333 • 0
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... Thanks you.
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written 6 months ago by
thomasjenner333 • 0
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... Hi,
I'm attempting to use 'enricher' and 'GSEA' functions from clusterprofiler package to analayze gene sets from MSigDB.
The following is the code I'm using:
> gmtfile <- "/path/c5.all.v6.1.entrez.gmt"
> c5 <- read.gmt(gmtfile)
> head(df)
ENTREZID log2FoldChange
1 1005169 ...
written 6 months ago by
thomasjenner333 • 0
• updated 6 months ago by
Guangchuang Yu • 1.0k
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... Hi Yu!
Thank you for responding. I tried what you've suggested, and got a list of pathways. Could you please explain why the previous parameters didn't work? Thanks once again.
...
written 6 months ago by
thomasjenner333 • 0
3
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... Hi,
I'm trying to do pathway analysis for DE porcine genes generated using DESeq2.
(A) I used package "clusterprofiler" to convert gene symbols to enterzids using the following code:
gg = bitr(m1, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Ss.eg.db")
geneSS <- as.vector(gg$ENTREZID)
...
written 6 months ago by
thomasjenner333 • 0
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... I'll look into the vignette. Thank you for responding.
...
written 7 months ago by
thomasjenner333 • 0
1
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183
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... Hi,
I'd used DESeq2 to get a list of differential expressed genes. Initially I had got the following results (showing a few records). The following was done a few months ago.
> res <- results(dds)
> res <- res[order(res$padj),]
> head(res)
log2 fold change (MAP): condition treated ...
written 7 months ago by
thomasjenner333 • 0
• updated 7 months ago by
Michael Love ♦ 19k
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