[BioC] Correlation matrix and pca on matrix with NA values

[James W. MacDonald]

Hi Daniel,

Daniel Brewer wrote:
> I have an expression matrix that contains NA values.  What is the best
> way to get:
> 1) prcomp()  (Exits with "Error in svd(x, nu = 0) : infinite or missing
> values in 'x'")
> 2) cor() (Exits with "Error in cor(exprs(Sperger)) : missing
> observations in cov/cor")
> to work with this type of matrix.

Take a look at the pcaMethods package.

Best,

Jim


> 
> Many Thanks
> 
> Dan
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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