Entering edit mode
3.2 years ago
fionajcunningham
•
0
Dear all, I am wondering if it is feasible to use a microarray - or should i ONLY use rna seq datasets to input into metascape. I am aware that the inputted gene list will be compared by metascape against the entire genome and so the microarray would not have that kind of coverage being confined to a discrete amount of genes predetermined. Please kindly advise if metascape is really only for rna seq high throughput sequencing data? thanks, Fiona.
The background/universe problem is also present for RNA-seq data. RNA-seq does not profile all the genes in the genome, principally because not all are expressed within any single cell. For example, say that you're analysing neurons by RNA-seq, you will tend to detect neuron-specific genes when you do differential gene testing, because those are the ones that are expressed and susceptible to change anyway. So if you do enrichment against the whole genome, there may be a bias towards detecting neuronal pathways.
I have never used metascape, but a quick google search shows that it may be possible to input a custom background: see this link. If that is the case, you could input there all your analysed genes (e.g. all the genes you tested in the microarray, or all the filtered genes you tested in the RNA-seq).
Thank you Papyrus appreciate this. F