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

[Daniel Brewer]

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.

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