User: thomasjenner333
thomasjenner333 • 0
- Reputation:
- 0
- Status:
- New User
- Location:
- Last seen:
- 8 months, 3 weeks ago
- Joined:
- 9 months, 3 weeks ago
- Email:
- t**************@gmail.com
Posts by thomasjenner333
<prev
• 7 results •
page 1 of 1 •
next >
0
votes
1
answers
409
views
1
answers
... 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
thomasjenner333 • 0
0
votes
1
answers
348
views
1
answers
... Thanks you.
...
written 9 months ago by
thomasjenner333 • 0
2
votes
1
answer
409
views
1
answer
... 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 9 months ago by
thomasjenner333 • 0
• updated 8 months ago by
Guangchuang Yu • 1.1k
0
votes
1
answers
348
views
1
answers
... 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
thomasjenner333 • 0
3
votes
1
answer
348
views
1
answer
... 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$ENTREZID)
...
written 9 months ago by
thomasjenner333 • 0
0
votes
1
answers
259
views
1
answers
... I'll look into the vignette. Thank you for responding.
...
written 9 months ago by
thomasjenner333 • 0
1
vote
1
answer
259
views
1
answer
... Hi,
I'd used DESeq2 to get a list of differential expressed genes. Initially I had got the following results (showing a few records). The following was done a few months ago.
> res <- results(dds)
> res <- res[order(res$padj),]
> head(res)
log2 fold change (MAP): condition treated ...
written 9 months ago by
thomasjenner333 • 0
• updated 9 months ago by
Michael Love ♦ 20k
Latest awards to thomasjenner333
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.2.0
Traffic: 302 users visited in the last hour