User: sugus
sugus • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- China Pharmaceutical University
- Last seen:
- 3 days, 7 hours ago
- Joined:
- 1 year, 8 months ago
- Email:
- 6********@qq.com
Posts by sugus
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... OMG it should be logical, how stupid I am....
Thanks for pointing out that and let me try.
...
written 12 days ago by
sugus • 20
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... Thanks Yu, but how to get detailed information for each pathway.
For example, GSEA output could be summary to a data frame with a lot of pathways, but gseaplot shall extract information from one of these pathway to plot figure, how to get this kind of information?
Thanks advanced. ...
written 12 days ago by
sugus • 20
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... Hi there,
Actually I have two questions,
First, how to extract detail information from a GSEA object derived from GSEA() {clusterPorfiler R package}.
Like the cmd:
GSEA.RES <- GSEA(geneList = geneList,TERM2GENE=MSigDB,seed = 111,verbose=F)
I have to use gseaplot and point the interested p ...
written 17 days ago by
sugus • 20
• updated
16 days ago by
Guangchuang Yu • 1.9k
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... Hi there,
I am trying to use chAMP pipeline to analysis EPIC methylation data.
In the chAMP pipeline, there is an embeded GSEA module called chAMP.gsea and it seems to support customized CpGlist or Genelist from its help document. (see the following CpGlist and Genelist)
Usage
cha ...
written 4 weeks ago by
sugus • 20
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... Hi there,
Is anyone use GenePattern and familiar with SubMap which used to compare expression data across two data.
I follow the instruction and made a label stating with 1 in 3rd line, and if there is any 0, the GenePattern will automatic add 1 to labels. However, I always get error to read cls ...
written 3 months ago by
sugus • 20
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Comment:
C: No result in enrichGO
... Yes, it works today.
So weird..... ...
written 4 months ago by
sugus • 20
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Comment:
C: No result in enrichGO
... No, this code just makes a more decent summary, but the result is still nothing. ...
written 4 months ago by
sugus • 20
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Comment:
C: No result in enrichGO
... Sure, here is the contents:
> de
[1] "4312" "8318" "10874" "55143" "55388" "991" "6280" "2305" "9493" "1062" "3868"
[12] "4605" "9833" "9133" "6279" "10403" "8685" "597" "7153" "23397" "6278" "79733"
[23] "259266" "1381" "3627" "270 ...
written 4 months ago by
sugus • 20
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... Hi, I am new to clusterProfiler and following the R documentation.
In the website instruction for enrichplot,
here is some demo for enrichGO:
library(clusterProfiler)
data(geneList, package="DOSE")
de <- names(geneList)[abs(geneList) > 2]
ego <- enrichGO(de, OrgDb = "org.H ...
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... Hi there!
I am using aheatmap to find some pattern but I need to reorder the dendrogram.
I find there is a function called reorder that seems to do this job but I am really having difficulty in understanding it.
I tried messing around with 'weights' for reorder, I thought when the anglo.fun = mean ...
written 5 months ago by
sugus • 20
• updated
5 months ago by
Kevin Blighe ♦ 28k
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