How to make GSEAplot with chip set
1
0
Entering edit mode
Seongsu • 0
@b6a4432b
Last seen 5 days ago
South Korea

Hi, I'm a beginner of R and Python, and also beginner of Bioinformatics. (I'm graduated school's student and I just start that few months ago) I'm finding best package for what I want to do.

I want to do GSEA and make GSEA plot by enrichplot package. (https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html)

My data has 'Affy probe ID', 'adj.P.Value', 'P.Value', 'log2FC', 'Gene.symbol' and 'Gene.title'... How can I do GSEA with Chip(Affy_U133) by my data?

If is it possible, I want to make same plots with GSEA software(Msigdb) May anyone recommend the packages for me?

And, if you know any good guide texts for beginner, I hope you send it to me!

Thank you for your help.

Choi

geneset GeneSetEnrichment msigdb • 157 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 16 hours ago
United States

The book you link to is 'a good guide text for beginners'. Have you read it?

0
Entering edit mode

I read it and ran, but the plots are different with GSEA software, so I'm finding the way for application the Chip

ADD REPLY

Login before adding your answer.

Traffic: 439 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6