Dear all,

I would like to compare three RNA-seq datasets of early plants, young plants, and old plants. These three datasets were prepared in different time points and techniques.

My question is how gene A changes over developmental time. Would it be possible to combine these three available data for analysis? How do you remove the batch effect before running Deseq2?

Thank you very much for sharing. Best regards, Yosapol

RNAseq is very sensitive to batch effect. If developmental stage and technical batch are totally confounded, there is no valid way to look at the data together. Any and every difference you see could 0% biological, and 100% caused by technical differences.