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st: vce matrix manipulation before and after pca

From   Sheela Athreya <>
Subject   st: vce matrix manipulation before and after pca
Date   Thu, 5 Aug 2010 20:33:52 -0500

I am trying to do the following in StataSE 11.1 for the Mac (OS 10.6) using a dataset comprised of 23 continuous variables (measurements of the skeleton) on 11,000 modern humans--a mixed sample of adult males and females.

1) Do a PCA of the males and females separately (I used the operation: "by SEX_CODED, sort : pca GOL-OAA")

2) Average the resulting vce matrices together

My question is:  how do I save the two vce matrices that are computed from these two pca's (one on each sex) and average them together to form one pooled-sex vce matrix? I don't know Mata so my question is related to doing this in Stata SE 11.1.

-I tried this using the command "matrix define ModPooledSex = __000001+__000000/2"--in other words, the two resulting matrices that were in memory, I added together and tried to divide by 2.   I got the error "000000 not found", even though that was one of the matrix names available in the pull-down menu under "define matrix from expression"--presumably it was one of two matrices automatically stored in memory.

When I tried to do the same thing again, I only saw one matrix (named 000000) in memory.  I am able to view that matrix, but not save or manipulate it at all.  

I have tried "estimates store", but can't retrieve the actual vce matrix to manipulate it or use it in other analyses.

My next question is: how can I then use a user-defined vce matrix (the pooled-sex one) and take another dataset entirely (of the same measurements, but different individuals, called Dataset2) and compute PC scores for Dataset2 based on the pooled-sex vce matrix from the modern human dataset?

I hope this isn't too confusing, or too basic.  I've been rooting around in all the documentation, the statalist archives, etc for hours before posting to the list, but I truly just can't figure it out.  Any help would be greatly appreciated.

Many thanks,

Sheela Athreya, Ph.D.
Department of Anthropology
Texas A&M University
College Station, TX  77843

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