Getting loadings of components from pcaMethods
Entering edit mode
Last seen 3.9 years ago

I want to get the loadings of components from pcaMethods.

To illustrate the problem, I have a matrix x

  a b c
1 ... ... ...
2 ... ... ...
3 ... ... ...


By loadings(x), I get

  PC1 PC2
a ... ...
b ... ...
c ... ...


However, I want to get

  PC1 PC2
1 ... ...
2 ... ...
3 ... ...


Anyone knows how to do that?

Thanks a lot!

pcamethods • 438 views
Entering edit mode
Last seen 3 hours ago
United States

It is conventional for high-throughput data to have samples in columns and reporters (genes, transcripts, whatever) in rows. In which case, when you get the loadings, what you should expect to get is the thing you get. What you want is (apparently) to get the loadings by gene, which doesn't make any sense - PCA is intended to collapse the gene information, so by definition you don't have anything by gene any more, because you have collapsed the data into linear combinations of the underlying gene expresssion.


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