PCA analysis

[wilson90]

Dear all,

I would like to use PCA to do initial subtyping of my RNA-Seq samples. But, I have questions regarding the loadings value (using prcomp in R).

It is fine if my loadings values for PC1(the one with the greatest variance) are less than 0.1 (magnitude)? or should I reduce the number of genes that I use in the analysis so that I can see increase in the loadings?

Thank you.

Wilson

[dpryan]

If the loading is <10%, then it wouldn't make sense to try to segregate according to that as it won't be very predictive. Just try to use the top N most variable genes and you'll likely get much more useful results.