User: thomasjenner333

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Posts by thomasjenner333

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Comment: C: Clusterprofiler - MSigDB gene set analysis - Updated
... 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. ...
written 8 months ago by thomasjenner3330
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Comment: C: ReactomePA - Pathway analysis for DE porcine genes
... Thanks you. ...
written 9 months ago by thomasjenner3330
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Clusterprofiler - MSigDB gene set analysis - Updated
... 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 ...
clusterprofiler gsea msigdb written 9 months ago by thomasjenner3330 • updated 8 months ago by Guangchuang Yu1.1k
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Comment: C: ReactomePA - Pathway analysis for DE porcine genes
... 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 9 months ago by thomasjenner3330
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ReactomePA - Pathway analysis for DE porcine genes
... 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$ENTREZID) ...
clusterprofiler reactomepa written 9 months ago by thomasjenner3330
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Comment: C: DESeq2 - MAP and MLE - log2FoldChange
...  I'll look into the vignette. Thank you for responding. ...
written 9 months ago by thomasjenner3330
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DESeq2 - MAP and MLE - log2FoldChange
... Hi,  I'd used DESeq2 to get a list of differential expressed genes. Initially I had got the following results (showing a few records). The following was done a few months ago. > res <- results(dds) > res <- res[order(res$padj),] > head(res) log2 fold change (MAP): condition treated ...
deseq2 written 9 months ago by thomasjenner3330 • updated 9 months ago by Michael Love20k

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