I downloaded from SRA all available transcriptome experiments from a nonmodel organism in order to perform comprehensive analyses. I want to analyze both sequences and differential expression. While the former seems feasible with different experiments, the latter concerns me a bit.
Is it methodologically safe to compare differential expression levels across different experiments? All of them are performed on Illumina machines, but with different technology levels (2000 / 2500 / 4000) and with different coverage.What steps do I have to perform in order to compare their transcription level? Can I pool them and do some sort of normalization?
If you'd have some reading to suggest me (papers that do an analogous analysis) it would be excellent as well.