I want to do some analysis with the GSVA function in R, but I want to ask you if the matrix should be just normalized with DESeq2 or also log trasformed. I did this passage:

dds_campione <- DESeqDataSetFromMatrix(countData=raw, 
                                       colData=condition_breakfast, 
                                       design=~ Campione)

smallestGroupSize <- 3
keep <- rowSums(counts(dds_campione) >= 10) >= smallestGroupSize
dds_campione <- dds_campione[keep,]

matriceFiltrata <- counts(dds_campione, normalized = TRUE)

risultati_ssGSVA_temba <- gsva(expr = as.matrix(matriceFiltrata), 
                       gset.idx.list = tebua)

Is it ok or I also have to log trasformed the matrix before the last passage? Thank you

Hi,

We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the GSVA package in Bioconductor 3.19, and in that case, you cannot anymore call the gsva() function in the way you're doing it in your code, you should build first a parameter object, please consult the vignette of GSVA and do not hesitate to ask here if you have questions on how to proceed calling gsva().

cheers,

robert.