[BioC] how to use principal component analysis in R
aedin.culhane at ucd.ie
Mon Jun 20 12:19:11 CEST 2005
We have provided a simple package for running PCA or correspondence
analysis in the bioconductor package made4.
It will accept most bioconductor data classes, a matrix or data.frame.
To run a PCA
This will give a plot of the eigenvalues, and the first two eigenvectors
of the cases (arrays) and genes. Only the genes at the ends of the axes
are labelled (to ease the visualisation). You can also use
To visualise the genes and arrays.
The package made4 required that ade4 is installed. If this is not, you
can install it using
>>> weinong han <hanweinong at yahoo.com> 06/18/05 2:10 AM >>>
Wish you have a nice weekend.
I want to run the two-dimensional principal-components analysis of
patient group using 174-gene signature set from Welch-T test to
separate the patient group, at the same time, I want to the plots of PCA
Anyone tried or not? please tell me the functions and scripts.
Any advice and suggestions will be much appreciated.
Thanks in advance.
hanweinong at yahoo.com
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