PCA in predefined Groups??

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PCA in predefined Groups??

SHAFI
Hi

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.

Thanks in advance
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Re: PCA in predefined Groups??

chuck.01
This post was updated on .
Without taking away all the fun of trial and error, and exploration in R... I will direct you to this website which I found invaluable when I first began to use R:

http://www.statmethods.net/advgraphs/axes.html

one way would be to use:
plot(Yourdata, type="n")
and then 3 text() or points() statements to plot the groups represented by different colors.

Good luck!

SHAFI wrote
Hi

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.

Thanks in advance