Hello,

For each sample, it is one of 2 tissues (med or cerv), one of three ages (p8, 6m, 12m), and one of three genotypes (WT, mdx, d52). Please see incomplete sample sheet below:

I have read the vignette and saw that it is recommended that users run samples from all groups together and then use the contrast argument, which I have done. However, I also read in the vignette to split the data when there is higher within group variability in certain groups. Looking at the PCA plot, it is apparent that there is high within group variability in all groups, but less so for the p8 (seen on the left). Thus, would it be recommended to split up the data by age?

It may be hard to tell in this plot because PC1 explains so much of the difference. The variability is not so stark as in other cases, and you only have n=3 per group to determine the dispersion anyway, so it's better to pool.

I would lean towards keeping the data all together.