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I do not understand the output of ssGSEA using GSVA package in R

Bioinformatics Asked by Sylvia Rodriguez on May 19, 2021

I am using the GSVA package in R to do single sample gene set enrichment analysis (ssgsea) using method = ssgsea. This works, but I do not understand the output.

My full code is too long to post here, but the output I get is summarised in the data.frame df below.

Why are all 1084 data points around -0.96, except for two, which are around 0.036? I expected an output similar to a normal distribution. Can anyone explain?

I liked this post, but it did not help me understand:

Intuitive explanation of GSVA analysis

 df <- data.frame(signature = c("-0.964276426", "-0.964247731", "-0.96419991", "-0.963820692", "-0.963819435", "-0.963818779", "-0.963816325", "-0.963816261", "-0.963815189", "-0.9638144", "-0.963813166", "-0.96381049", "-0.963809529", "-0.96380853", "-0.963808015", "-0.963806952", "-0.963804683", "-0.96380347", "-0.963803246", "-0.963803246", "-0.963803246", "-0.963803246", "-0.963803246", 
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