User: sugus

gravatar for sugus
sugus20
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

<prev • 22 results • page 1 of 3 • next >
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Comment: C: GSEA results change in clusterProfiler
... OMG it should be logical, how stupid I am.... Thanks for pointing out that and let me try. ...
written 12 days ago by sugus20
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Comment: C: GSEA results change in clusterProfiler
... 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 sugus20
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GSEA results change in clusterProfiler
... 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 ...
clusterprofiler gsea written 17 days ago by sugus20 • updated 16 days ago by Guangchuang Yu1.9k
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How to customized CpGlist or Genelist in chAMP.gsea
... 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 ...
gsea champ written 4 weeks ago by sugus20
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SubMap in GenePattern
... 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 ...
genepattern submap cls written 3 months ago by sugus20
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Comment: C: No result in enrichGO
... Yes, it works today. So weird..... ...
written 4 months ago by sugus20
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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 sugus20
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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 sugus20
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No result in enrichGO
... 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 ...
R enrichgo clusterprofiler written 4 months ago by sugus20 • updated 4 months ago by szhaoaf30
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Reorder dendrogram for a better heat map
... 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 ...
R dendrogram reorder written 5 months ago by sugus20 • updated 5 months ago by Kevin Blighe28k

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