R help - Dec 2007 - Principal Components Analysis

Hi,

I do have a file that has 500000 columns and 40 rows. I want to apply PCA on
that data and this is what I did

h1<-read.table("Ccode.txt", sep='\t', header=F) # reads the
data from the
file Ccode.txt
 h2<-prcomp(na.omit(h1),center=T)
 
but I am getting the following error
 
"Error in svd(x, nu = 0) : 0 extent dimensions"


I appreciate if someone can help

Thanks

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Are there lots of missing values in the data? If so, my guess would be that
na.omit(h1) leaves you with no data. Have you checked this?

Bert Gunter
Genentech

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On
Behalf Of SNN
Sent: Wednesday, December 26, 2007 2:49 PM
To: r-help at r-project.org
Subject: [R] Principal Components Analysis


Hi,

I do have a file that has 500000 columns and 40 rows. I want to apply PCA on
that data and this is what I did

h1<-read.table("Ccode.txt", sep='\t', header=F) # reads the
data from the
file Ccode.txt
 h2<-prcomp(na.omit(h1),center=T)
 
but I am getting the following error
 
"Error in svd(x, nu = 0) : 0 extent dimensions"


I appreciate if someone can help

Thanks

-- 
View this message in context:
http://www.nabble.com/Principal--Components-Analysis-tp14507365p14507365.htm
l
Sent from the R help mailing list archive at Nabble.com.

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On Wed, 26 Dec 2007, SNN wrote:
>
> Hi,
>
> I do have a file that has 500000 columns and 40 rows. I want to apply PCA
on
> that data and this is what I did
>
> h1<-read.table("Ccode.txt", sep='\t', header=F) #
reads the data from the
> file Ccode.txt
> h2<-prcomp(na.omit(h1),center=T)
>
> but I am getting the following error
>
> "Error in svd(x, nu = 0) : 0 extent dimensions"
>
>
> I appreciate if someone can help
You probably have a missing value in every row.  But does PCA with 500000 
columns make sense: 4999961 of the PCs are constant and arbitrary?
It is possible you meant PC on the transpose (sometimes called Q-mode)

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595