Hi all,
I'm currently analysing some RNAseq data and my colleague has asked about pair wise comparisons. I'm still very new to bioinformatic analysis, having only started a couple of months ago on it, so wanted to seek some advice and guidance.
In the study, he has 3 samples of 2 conditions (wild type, and mutant). The RNA from each paired set of samples (1 WT and 1 mutant) were extracted on the same day, and the different pairs on different days.
The RNAseq was performed, and they seem to cluster in their respective pairs, but with some (more than i'd want to see) variability between the pairs. Is it possible to perform differential expression to take into account these paired samples, I've done DEseq on the 6 samples all together. Thanks in advance
Thank you so much, I'll give that a go :)