I am Prathyusha Bachali, student at UNCC. I am trying to work with GSVA package. I have created my geneset collection object and now I am trying to use GSVA function by giving expressionset which is basically all positive values of genes by sample and my geneset collection object which is collection of list of genesets with geneSymbol as identifier. My gsva function is working fine, but I am not able to interpret my results or I am not sure how GSVA score has been calculated here. Because the result, I obtained after running GSVA has some negative and positive scores. What does negative score represent here?
Here is my input expressionset object. There are 1819 genes with expression values.
geneSymbol CTL1 CTL2 SLE1 SLE2
ESRRA 6.683 6.525 6.461 6.392
CAPNS1 10.591 10.047 11.52 11.86
After performing gsva on my expressionset matching with GenesetCollection object, I got the follwong output with few negative scores. I believe these are GSVA enrichment scores.
geneSet CTL1 CTL2 SLE1 SLE2
Immunescreen 0.012 -0.1264 -0.2167 -0.2767
ISG -0.032 0.02867 0.057 -0.078
Thanks in advance. Any help is much appreciated.