Table 3.

Main advantages and disadvantages of gene expression detection assays.

	Advantages	Disadvantages
qRT-PCR	a popular technology, low cost	only for small number of genes
Microarray	works for more than 1000 genes, commercial chip/arrays ready to use	requires expertise for data normalization and analysis
NanoString	standard workflow and analysis pipeline are setup by the company	machine is costly, constrained by one company
RNA-seq	whole transcriptome, MiSeq pipeline for data analysis	machine is costly, requires expertise for lib prep and sequencing
FISH	localizes and detects gene expression	complicated procedure
TMA	detects hundreds of samples simultaneously	mainly for research, not for clinical settings