I am studying bioinformatics for my research and I have some questions regarding RNA seq vs. Microarray for gene expression level.
When considering their pros and cons, I think that RNA-seq has more good advantages over Microarray. For example, RNA is available for all species and also can check novel transcribed regions because RNA-seq platform doesn't require pre-defined procedures for checking gene expression level.
And also RNA has good advantages which are alternative splicing and to identify fusion genes. However, I didn't get the reason why RNA-seq has such two good points (alternative splicing, fusion genes) over Microarray techniques.
The two things you aren't sure about are due to microarrays only being able to detect exactly what they were designed for. In the case of fusion genes, to detect that on a microarray you'd have to have a probe spanning the fusion point. Similarly, for alternative splicing, you can only detect what you've designed probes for. That's one of the biggest gains with RNAseq, you can find things that you didn't explicitly want to look at beforehand.
I should note that the only real downside to RNAseq is that signals from genes/transcripts/etc. are competitive. So if you ever want to deconvolve signals originating from multiple sources (e.g., you have heterogenous samples and are interested in differential expression due to something within each of the sources rather than simply between treatment groups) then this is simpler with microarrays (i.e., things like independent component analysis are simpler).
Competitiveness is an innate part of sequencing (unless you have really low input and don't amplify it much), cluster number is small compared to the number of fragments available to bind to them.
Hi Devon, could you please give me some suggestions or comments about the advantage of microarrays? Because I'm just using the microarray data instead of rna-seq, I have to explain some advantage of them. Or could you please give me some papers for me to read about this issue? Thank you.
These are completely different techniques, they supplement each other in some ways, but they are different in nature. Microarray expression catches some time moment of a predefined gene set and sequence analysis can cover the entire genome, however, processing and annotation is prone to losing the truth.
You can find free books on topic on 4shared.com and www.libgen.org and on amazon and abebooks, of course.
Hi Devon, could you clarify the second part (downside) a little more? What feature of RNA-Seq makes the signals competitive?
Competitiveness is an innate part of sequencing (unless you have really low input and don't amplify it much), cluster number is small compared to the number of fragments available to bind to them.
Hi Devon, could you please give me some suggestions or comments about the advantage of microarrays? Because I'm just using the microarray data instead of rna-seq, I have to explain some advantage of them. Or could you please give me some papers for me to read about this issue? Thank you.