Hello, I have 8 samples (4 WT and 4 mutants). I have performed bulk RNA seq on these (Kallisto, and then DESeq2) I am attaching my PCA plot, I was expecting the wild type to cluster together and all the mutants to be together, but this was not the result. Does it indicate that my samples have a lot of variance?
Can anyone suggest to me any other method/plot that can represent my WT vs mutant samples?
I would really appreciate it.
How much variance were explained by PC1 and PC2? It doesn't look like that the largest source of variation came from the genotype difference.
Cross posted here (including the code used to make up the counts):
https://support.bioconductor.org/p/9157911/#9157959