I was doing a comparison between gene expressions for TCGA data obtained from microarrays and rna sequencing. I downloaded normalized data from firebrowse and when comparing gene names in those two platforms, I noticed that there are nearly 1000 genes that are present in microarray data but not in rna-seq data. It's in contradiction with my understanding of rna sequencing because I think that rna sequencing must give us whole transcriptome! So why there are genes that are not present in TCGA normalized rna-seq data?
(Sorry, I am begginner in bioinformatics!)