Hope all you are having a good day :)
I was curious to understand how to analyse rna-seq data coming from multiple experiments using Deseq2. So initially I had 3 disease vs 3 controls and this is how they clustered on a PCA plot :
Then I started looking into a second batch that has 5 disease vs 4 controls :
And ultimately when I want to analyse (differential gene expression analysis) all 15 samples at once this is how they cluster on the PCA plot :
The design formula is as follows :
design = ~batch + condition
The sequencing depth is different in both the batches. Can I incorporate quantile normalization on the data to reduce the variance between the same conditions?
Please let be know how I could go about it. Thanks in advance.
Have a lovely day :)