Error in running gsva function from GSVA package
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@momeneh-foroutan-7398
Last seen 5.6 years ago
Australia

Hi all,

I have a gene signature (about 300 genes) including up- and down-regulated gene sets, and would like to use package GSVA to assess my signature on samples from a matrix (18000 genes in row and 600 patient samples in columns). The row names of the matrix as well as the gene sets are both gene symbols (I can use Entrez ID if it matters?). I am following the instruction here "https://www.bioconductor.org/packages/devel/bioc/vignettes/GSVA/inst/doc/GSVA.pdf"

I've tried both "gsva" and "ssgsea", however, in both cases I get error.

In the below codes m is a matrix, and for performing "gsva", geneSet is a list consisting of two signatures (up and down gene sets) while for the "ssgsea" method, geneSet is a list containing only one signature:

es.dif <- gsva(m, geneSets, mx.diff=1, verbose=FALSE, parallel.sz=1)$es.obs

es.dif <- gsva(m, as.list(geneSet), method="ssgsea", mx.diff=1, verbose=FALSE, parallel.sz=1)

Error in if (any(sdGenes == 0)) { : missing value where TRUE/FALSE needed

I should say that even changing the class of my matrix to ExpressionSet did not work for me... I searched on Bioconductor as well but could not find my answer... Any help would be highly appreciated.

By the way, here is the output of my session information:

sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] GSVA_1.12.0          GSEABase_1.26.0      graph_1.42.0        
 [4] annotate_1.42.1      AnnotationDbi_1.26.1 GenomeInfoDb_1.0.2  
 [7] Biobase_2.24.0       BiocGenerics_0.10.0  BiocInstaller_1.14.3
[10] biomaRt_2.20.0      

loaded via a namespace (and not attached):
[1] bitops_1.0-6    DBI_0.3.1       IRanges_1.22.10 RCurl_1.95-4.7 
[5] RSQLite_1.0.0   stats4_3.1.1    tools_3.1.1     XML_3.98-1.3   
[9] xtable_1.8-0   

Many thanks in advance,

Sepideh.

 

gsva • 1.6k views
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Robert Castelo ★ 2.7k
@rcastelo
Last seen 12 weeks ago
Barcelona/Universitat Pompeu Fabra

Hi Sepideh,

you are running GSVA version 1.12.0 but the latest version of GSVA  is 1.18.0. Looking at the error and the related source code, I'm pretty sure this error was fixed in a previous release of the GSVA package, and therefore, when you update to the latest version this error should not show up again. Let me know otherwise by replying to this answer.

To update to the latest Bioconductor release (3.2) that includes the latest GSVA 1.18.0 please go to http://bioconductor.org/install and follow the instructions there.

cheers,

robert.

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Many thanks Robert,

In fact, it solved the problem :-) I don't get the error anymore... however, I get warnings and I am not sure whether I should be worried about them? The warnings say that I have some genes with constant values across all samples. Please look at them:

By running "gsva" method, I get:

Warning messages:
1: In .local(expr, gset.idx.list, ...) :
  536genes with constant expression values throuhgout the samples.
2: In .local(expr, gset.idx.list, ...) :
  Since argument method!="ssgsea", genes with constant expression values are discarded.

By performing "ssgsea", I get similar warning:

Warning message:
In .local(expr, gset.idx.list, ...) :
  536genes with constant expression values throuhgout the samples.

Should I remove some of the genes before using the package? 

Thanks again for your time on answering my question :-)

Cheers,

Sepideh

 

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