GSVA for single sample
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jaison75 ▴ 20
@jaison75-9008
Last seen 3.6 years ago
United States

Hello,

I am trying to use GSVA to calculate an enrichment score for a single sample.  I thought the ssgsea method implemented in GSVA can perm such a calculation.  Do I have this wrong?  My searches have returned empty handed.  I am pasting an example code below I used to test the concept (modifed from the help page). 

 

## consider three disjoint gene sets
geneSets <- list(set1=paste("g", 1:3, sep=""),
                 set2=paste("g", 4:6, sep=""),
                 set3=paste("g", 7:10, sep=""))

y1 <- as.matrix(runif( n = 10, min = 5.3, max = 15),ncol =1)
colnames(y1) <- c("s1")
row.names(y1) <- paste("g", 1:10, sep="")
gsva(y1, geneSets, method == "ssgsea", ssgsea.norm = FALSE, mx.diff = FALSE, kernel = F)

Any help would be appreciated.

 

Thanks

-Jaison

gsea gsva ssgsea • 898 views
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Entering edit mode
Robert Castelo ★ 2.7k
@rcastelo
Last seen 27 minutes ago
Barcelona/Universitat Pompeu Fabra

hi,

you have a typo in your code, the '==' operator is for comparison, not for assignment. please replace

method == "ssgsea"

by

method = "ssgsea"

and it will work.

cheers,

robert.

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Entering edit mode
jaison75 ▴ 20
@jaison75-9008
Last seen 3.6 years ago
United States

Thank you very much Robert.  I cannot believe, I did not catch that. 

This solved the issue.

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