I'm currently trying to calculate a signature score for immune cells in the tumor environment using RNAseq data from the TCGA database. To do so, I'm using the TCGAbiolinks and GVSA package:
query.gbm <- GDCquery(project = "TCGA-GBM", data.category = "Gene expression", data.type = "Gene expression quantification", platform = "Illumina HiSeq", file.type = "normalized_results", experimental.strategy = "RNA-Seq", legacy = TRUE) data <- GDCprepare(query.gbm) gene_expression <- assay(data) mic <- c("Epb41l5","Ysk4","Fam72a","Cdk18","Adora1","Olfml2b","Slamf1","Sccpdh","1110021L09Rik","Ank3","Kitl","Pmel","Sec14l2","Snap47","Zfp867","Fam83g","Rab34","Sarm1","Leprel4","Hsd17b1","Plekhh3","Etv4","Rundc3a","Ccdc46","Apob","Wdr35", ...) genelist_mic <- list(mic) score <- gsva(gene_expression, genelist_mic, method= "ssgsea", rnaseq=TRUE, abs.ranking=FALSE, min.sz=1, max.sz=Inf, no.bootstraps=0, bootstrap.percent = .632, parallel.sz=0, parallel.type="SOCK", mx.diff=TRUE, tau=switch(method, gsva=1, ssgsea=0.25, NA), kernel=TRUE, ssgsea.norm=TRUE, verbose=TRUE)
Everything seems to work just fine. I get an expression matrix with gene ids in rows and samples in the corresponding columns but I always get the following error message for the gsva() function:
Error in .local(expr, gset.idx.list, ...) : No identifiers in the gene sets could be matched to the identifiers in the expression data.
If I adjust my gene list (genelist_mic) to some of the gene identifiers from my gene expression matrix (gene_expression) that I get from TCGA, the code works. I also checked the gene identifiers of both the gene expression matrix and my cell type specific gene list with the David tool and it looks like they are all Gene Official Symbols. So I don't understand why it doesn't recognize the gene identifiers.
The gene identifiers from the gene expression matrix that I get back from TCGA look like this:
A1BG A2M NAT1 NAT2 RP11-986E7.7 SERPINA3 AADAC AAMP AANAT AARS ABAT ABCA1 ABCA2 ABCA3 ABCB7 ABCF1
Does anyone know why this might happen?
I would highly appreciate your help!