Combining RNA-seq data

Question

[itunu08]

Hello,

I downloaded two RNA seq datasets for an organism from ArrayExpress. Is it okay to combine these two datasets to make my analysis more robust? They both cover same conditions and used same sequencing technology but the inter-spacing of the time points are different.

Thanks

[Biomonika (Noolean)]

You should move this question from "Forum" to "Question"

[itunu08]

done! thanks

Answer 1

[Chirag Nepal]

If the time points are different, you should not merge them. At different time points, many genes are expressed differently, hence you should not combine them.

Answer 2

[Devon Ryan]

This depends a bit on the type of analysis you're doing. These will likely differ from your samples due to being prepared elsewhere, so that could throw things off. It's likely that you'll want to do a PCA or run things through SVAseq or Combat.

Answer 3

[mikhail.shugay]

My point is that given that both experiments have enough time points the most robust conclusion would be the one that was replicated separately in both time courses. Combining datasets could increase the statistical power of the analysis, yet the major drawback could be possible batch-effects if those experiments are not properly normalized.

[Arindam Ghosh]

Is COMBAT sufficient to remove batch effects from this type of study?