I downloaded TCGA BRCA RNAseq data from UCSC cancer browser or used TCGAbiolinks:
library(TCGAbiolinks) query <- GDCquery(project = 'TCGA-BRCA', data.category = 'Transcriptome Profiling', data.type = 'Gene Expression Quantification', workflow.type = 'HTSeq - Counts') GDCdownload(query) brca.seq <- GDCprepare(query)
And checked the expression of SOX10:
library(DESeq2) r = rowData(brca.seq) as.numeric(assay(brca.seq[which(r$external_gene_name == 'SOX10'),]))
It turns out its expression is zero in all patients. But in data from UCSC cancer browser (HiSeqV2) SOX10 average expression is 6. The data from UCSC can be found here: https://tcga.xenahubs.net/download/TCGA.BRCA.sampleMap/HiSeqV2.gz
Another question, TCGAbiolinks is more updated than UCSC caner browser as it directly downloads data from TCGA right?