Question: Correlation matrix and pca on matrix with NA values
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gravatar for Daniel Brewer
12.4 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}}
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ADD COMMENTlink modified 12.4 years ago by Aedin Culhane510 • written 12.4 years ago by Daniel Brewer1.9k
Answer: Correlation matrix and pca on matrix with NA values
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gravatar for Aedin Culhane
12.4 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
ADD COMMENTlink written 12.4 years ago by Aedin Culhane510
Answer: Correlation matrix and pca on matrix with NA values
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gravatar for James W. MacDonald
12.4 years ago by
United States
James W. MacDonald50k 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.
ADD COMMENTlink written 12.4 years ago by James W. MacDonald50k
Answer: Correlation matrix and pca on matrix with NA values
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gravatar for Wolfram Stacklies
12.4 years ago by
Wolfram Stacklies10 wrote:
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ADD COMMENTlink written 12.4 years ago by Wolfram Stacklies10
That works well. Thanks. I am happy to stick with that, but I still do not understand why I get the error message "Error in svd(x, nu = 0) : infinite or missing values in 'x'", because looking at prcomp it should omit those genes that contain NA values when na.action=na.omit. I am interested in sample PCR, so there should be plenty of information left to do this. Any ideas? Dan Wolfram Stacklies wrote: > Hi Daniel, > > I am the maintainer of the pcaMethods package. The package provides several > PCA implementations that can handle missing data, so this should solve your > problem. Maybe you want to have a look at the ppca (probabilistic pca), > from > my experience it produces nice results. > You should take care about the amount of missing data, or or rows / > columns that > contain large numbers of missing values. For these the estimation may not be > very accurate (as there is little information to base the estimate on). > Better remove > them first... > If there are further questions I will be happy to answer them. > There will be a new release of the package coming with the new Bioconductor > release. This version contains many improvements, maybe you want to have > a look. > > Regards, > Wolfram > > > On 4/10/07, *Daniel Brewer* <daniel.brewer at="" icr.ac.uk=""> <mailto:daniel.brewer at="" icr.ac.uk="">> 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 ************************************************************** 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}}
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