DESeq2 after GSVA "some values in assay are negative"

Question

[dew]

Dear guys,

Do you have experience that when you are done GSVA, get the gene set per sample matrix and want to use Deseq2 to find the differential expressed gene sets, while Deseq2 would appear the error " Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative", while the results from GSVA do have negative values.... how to deal with this, thanks a lot!

Best,

[jv]

It is common to do a statistical test to look for changes in gene set enrichment using the output of GSVA as input, however I recommend you follow the GSVA tutorial example which uses alimma workflow. As was pointed out here and by DESeq2, the output of GSVA is not a suitable format for input into DESEq2.

For details, see https://bioconductor.org/packages/release/bioc/vignettes/GSVA/inst/doc/GSVA.html#62_Differential_expression_at_pathway_level

[dew]

Thanks a lot for your kind guidance! Much appreciate!