I want to check the gene expressions of two family of plants. What are the methods that I can use? I also want to know the limitations. A discussion on this topic is expected.
That depends on the number of genes you want to analyze and the (financial) resources availible. For a small set of genes qRT-PCR or semiquantitative RT-PCR might be sufficient while for the entire transcriptome RNAseq might be the way to go. In between there are lots of possiblities...To get a useful answer to this question you might want to add more details....
I agree with Anja that you need to specify the number of genes to analyse. qRT-PCR is great if you don't have too many genes to examine. There are indeed many possibilities, We will be using Nanostring in a new project next year- this can similtaneously count transcripts of up to 800 genes.