Question: Correlation matrix and pca on matrix with NA values
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12.7 years ago by
Daniel Brewer1.9k
Daniel Brewer1.9k 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. Many Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}
cancer • 6.1k views
modified 12.7 years ago by Aedin Culhane510 • written 12.7 years ago by Daniel Brewer1.9k
Answer: Correlation matrix and pca on matrix with NA values
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12.7 years ago by
Aedin Culhane510
United States
Aedin Culhane510 wrote:
Hi Dan You could use nipals PCA. NIPALS analysis allows PCA of data sets with missing values. R code is available from http://biom3.univ-lyon1.fr/R/html/additifs.html Aedin
Answer: Correlation matrix and pca on matrix with NA values
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12.7 years ago by
United States
James W. MacDonald52k wrote:
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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
Answer: Correlation matrix and pca on matrix with NA values
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12.7 years ago by
Wolfram Stacklies10 wrote:
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