I downloaded microaaray and rna-seq data for breast cancer of the TCGA project from the firehose portal. When I computed the correlation between expression of each gene in different patients, correlation was high, as I expected. Correlation mean was 0.65 and median was 0.75. Intrestingely there exist genes with 0.-24 correlation between what is reported by microarray and what is reported by rna-seq.
But when I look at correlation between these two methods at one or some samples(patients), I observe near zero correlation. And when I plot the rna-seq vs microarray for these samples, I get a shape nearly like a rectangle!
Am I doing something wrong? I downloaded normalized data for both technologies, but I used log(rna-seq) in my analysis.
Edit: Agilent G450A_07 arrays vs Illumina Hiseq (RSEM normalized)