[BioC] Problems with COPA

[James W. MacDonald]

Hi Francesca,

Francesca Guana wrote:
> Dear Bioconductor users,
> 
> I'm trying to use the function copa (from the package copa in bioconductor
> 1.8) to detect recurrent chromosomal rearrangements in a set of 67 cancer
> samples, with respect to 14 normal samples. I loaded the data from an
> external .txt table (81 samples, 19665 genes), with no missing data, but
> when I run the function it gives me this error message:
> "error in quantile.default(num.out, probs = pct) :
>         missing values and NaN non allowed if 'na.rm' is FALSE"
> 
> I think that this quantile function is used inside the copaFilter function,
> but I cannot do anything since it is an internal function.
> 
> Can somebody help me?

I will need some more information before I can help. What arguments did 
you use in your call to copa()?

Best,

Jim


> 
> Thank you
> 
> Francesca Guana
> 
> --
> Cancer Genomics Lab
> Fondo Edo Tempia
> via Malta 3, 13900 Biella (Italy)
> phone: +39 015351830
> fax: +39 01521116
> email: francesca.guana at gmail.com
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
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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