This has a simple answer but it has been eluding me nonetheless.

I have been trying to build a PCA plot from scratch with the ability to plot predefined groups in different colors. I can plot PCA but I want it to plot with predefined groups (samples) with top 100 expressed genes. I have three groups. Can any body help me keeping in mind that the user is just beginner in R?

Actually I have miRNA data from affymetrix chip. Data is classified into 3 groups. I used limma package for analysis. I did RMA normalization, eBayes etc. But I did not get any miRNA significatly expressed in any group. When I posed questions about it on net somebody suggested me to PCA analysis etc. to remove outliners and go ahead with normal analysis as I did.

Now I will appreciate it some body can guide me from the begining