Hi, I have a question regarding differential gene expression analysis when the samples library method is different.
I have 10 samples total, 3 from one condition and 7 from the other. Among the first 3, 2 where sequenced using poly-a and one with ribo depletion library preparation method. In the other group I also have a mixture of them, but I could obtain more and make them all from the same method (any of them).
My question is if it is still possible to perform differential gene expression or if the library preparation method is a source of bias so big that leads to unreliable results.
Thank you very much in advance! Best, Daiana
Thank you kristoffer! I will definitely use this!
Update below, even Batch Effect removal was not enough