User: thomasjenner333

Reputation:
0
Status:
New User
Last seen:
1 year, 5 months ago
Joined:
1 year, 6 months ago
Email:
t**************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by thomasjenner333

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answer
701
views
1
answers
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 18 months ago by thomasjenner3330
0
votes
1
answer
533
views
1
answers
Comment: C: ReactomePA - Pathway analysis for DE porcine genes
... Thanks you. ...
written 18 months ago by thomasjenner3330
2
votes
1
answer
701
views
1
answer
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 18 months ago by thomasjenner3330 • updated 18 months ago by Guangchuang Yu1.1k
0
votes
1
answer
533
views
1
answers
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 18 months ago by thomasjenner3330
3
votes
1
answer
533
views
1
answer
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$ENTREZID) ...
clusterprofiler reactomepa written 18 months ago by thomasjenner3330
0
votes
1
answer
507
views
1
answers
Comment: C: DESeq2 - MAP and MLE - log2FoldChange
...  I'll look into the vignette. Thank you for responding. ...
written 19 months ago by thomasjenner3330
1
vote
1
answer
507
views
1
answer
DESeq2 - MAP and MLE - log2FoldChange
... Hi,  I'd used DESeq2 to get a list of differential expressed genes. Initially I had got the following results (showing a few records). The following was done a few months ago. > res <- results(dds) > res <- res[order(res$padj),] > head(res) log2 fold change (MAP): condition treated ...
deseq2 written 19 months ago by thomasjenner3330 • updated 19 months ago by Michael Love25k

Latest awards to thomasjenner333

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 255 users visited in the last hour