Microarrays have achieved its technological limits and hence in many studies mircoarrays are increasingly replaced by RNA sequencing.
does not require a priori knowledge of the RNA sequence
discover novel transcripts (gene finding)
detect single nucleotide polymorphisms (SNPs)
increasing accuracy
provides absolute transcript levels (more precise than hybridization)
no cross-hybridization issues
larger range from small to high expression levels
better accuracy in very small and very large values
But RNA-seq is still more expensive than microarray technology and requires higher computational resources for storing and analyzing the data.
https://www.illumina.com/technology/next-generation-sequencing/mrna-seq.html