[BioC] snapCGH - subscript out of bounds

[João Fadista]

Ok, thanks for the useful information.


Best regards

João Fadista
Ph.d. student


UNIVERSITY OF AARHUS
Faculty of Agricultural Sciences
Research Centre Foulum
Dept. of Genetics and Biotechnology
Blichers Allé 20, P.O. BOX 50
DK-8830 Tjele

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-----Original Message-----
From: J-C. Marioni [mailto:jcm68 at hermes.cam.ac.uk] 
Sent: Wednesday, February 07, 2007 11:28 AM
To: João Fadista
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] snapCGH - subscript out of bounds

Hi Joao,

Assuming that a and b refer to the Cy3 and Cy5 channels respectively, then I think using the design 1 1 1 -1 -1 -1 should work. The design component in snapCGH is only for stating whether the test sample is in the
Cy3 (-1) or Cy5 (1) channel respectively.

Hope this helps,
John


On Wed, 7 Feb 2007, João Fadista wrote:

> Dear all,
>
> I was trying to use the function processCGH from the snapCGH package with my MAList but it gave me this error:
> "Error: subscript out of bounds".
> Then, I changed my design and now it appears to be working. But this is a wrong design for my MAList.
>
> Right design that didn´t worked:
>      a  b
> 1    0  -1
> 2    0  -1
> 3    0  -1
> 4   -1   0
> 5   -1   0
> 6   -1   0
>
> Wrong design that worked:
> 1 1 1 1 1 1
>
> Thanks in advance
>
> Med venlig hilsen / Regards
>
> João Fadista
> Ph.d. studerende / Ph.d. student
>
>
>
> 	 AARHUS UNIVERSITET / UNIVERSITY OF AARHUS Det 
> Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences 
> Forskningscenter Foulum / Research Centre Foulum Genetik og 
> Bioteknologi / Dept. of Genetics and Biotechnology Blichers Allé 20, 
> P.O. BOX 50 DK-8830 Tjele
>
> Tel:	 +45 8999 1900
> Direct:	 +45 8999 1900
> Mobile:	 +45
> E-mail:	 Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk>
> Web:	 www.agrsci.dk <http://www.agrsci.dk/>
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