Question: creating a data file for GSVA analysis
gravatar for Sathya
5.4 years ago by
Sathya30 wrote:

I would like to use GSVA for enrichment analysis. By default, GSVA uses c2BroadSets data. Instead of c2BroadSets, I wanted to use c7Broadsets which is immune specific enrichment data. How to proceed with this?? 

Note: There are few blogs which talks about creating c5data using the gmt file available in molecular signature database. But, I have no clue how to proceed with that. Please let  me know.


gsva • 2.5k views
ADD COMMENTlink modified 3.6 years ago by dpenaherrera0 • written 5.4 years ago by Sathya30

Any update on this, Sathya? I actually would like to do the exact same analysis with the C7Broadset.



ADD REPLYlink modified 12 weeks ago by RamRS25k • written 4.3 years ago by balli.dave0
gravatar for dpenaherrera
3.6 years ago by
dpenaherrera0 wrote:

You have to first go to the MSigDB downloads page. Once you login, scroll down to the section labelled "c7: immunologic signatures gene sets" and download the appropriate .gmt file. Then import the data into R with a command similar to the following:

myC7 <- getGmt("c7.all.v5.1.entrez.gmt")

If you get an error, you might need to specify the other parameters of getGmt:

myC7 <- getGmt("c7.all.v5.1.entrez.gmt", geneIdType=EntrezIdentifier(), collectionType=BroadCollection(category="c7"), sep="\t")
ADD COMMENTlink modified 12 weeks ago by RamRS25k • written 3.6 years ago by dpenaherrera0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1525 users visited in the last hour