GSVA error - incomplete instalation?
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thrabe • 0
@thrabe-9205
Last seen 5.7 years ago
United States

Hi there,

I am trying to get the ssgsea algorithm running that is in the gsva package. I am reading an affymatrix dataset for this, convert it to an ExpressionSet object and then run the function. However, I get this error :

allFiles <- list.files('./affymatrix/TisMix_WTGene1_CEL/',full.names=TRUE,pattern = "\\.CEL\$")
expressionSet <-rma(Data)

result <- gsva(expressionSet,'ssgsea')

Error in (function (classes, fdef, mtable)  :
unable to find an inherited method for function ‘gsva’ for signature ‘"ExpressionSet", "character"’

Any ideas? GSVA documentation says it can be an expressionSet.

GSVA ExpressionSet • 1.4k views
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@james-w-macdonald-5106
Last seen 4 hours ago
United States

The error actually says something slightly different than what you think. It says it can't find a method for a signature that consists of an ExpressionSet and a character. If you look at the help for gsva(), it says this about the second argument:

gset.idx.list      Gene sets provided either as a list object or as a GeneSetCollection object.

You have to pass in both an ExpressionSet and a list of gene sets, or a GeneSetCollection in order for the function to work. In addition, if you want to use the ssgsea method, you have to use  method = "ssgsea" in your function call. The only time you can use positional argument matching is if you have already passed in objects for the first three arguments as well (e.g., methods is the fourth argument, so R will only know that 'ssgsea' is intended for the fourth argument if there are three arguments ahead of it in the function call).

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How do I get the gset.idx.list when reading the data from CEL files?

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You don't. The gset.idx.list is something that you have to supply yourself. This can be a list object, or a GeneSetCollection. The GeneSetCollection is defined in the GSEAbase package, and you can use that package to make GeneSetCollections, or to get them from e.g., the Broad Institute. See the GSEAbase vignette for more information.

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GSVA transforms a gene-by-sample expression data matrix into a geneset-by-sample expression data matrix. You should know beforehand what gene sets are do you want to use and this depends on your research question at hand. The GSVA package itself has the C2 collection of MSigDB gene sets version 3.0 that you can load by typing:

Section 4 of the GSVA vignette gives an example using those gene sets.

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thrabe • 0
@thrabe-9205
Last seen 5.7 years ago
United States
How do I get the gset.idx.list when reading the data from CEL files?