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, Jo?o 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
>
> Jo?o 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 All? 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=""/>
> ________________________________
>
> Tilmeld dig DJF's nyhedsbrev / Subscribe Faculty of Agricultural
Sciences Newsletter <http: www.agrsci.dk="" user="" register?lan="dan-DK"> .
>
> Denne email kan indeholde fortrolig information. Enhver brug eller
offentligg?relse af denne email uden skriftlig tilladelse fra DJF er
ikke tilladt. Hvis De ikke er den tilt?nkte adressat, bedes De
venligst straks underrette DJF samt slette emailen.
>
> This email may contain information that is confidential. Any use or
publication of this email without written permission from Faculty of
Agricultural Sciences is not allowed. If you are not the intended
recipient, please notify Faculty of Agricultural Sciences immediately
and delete this email.
>
>
>
> [[alternative HTML version deleted]]
>
>
Ok, thanks for the useful information.
Best regards
Jo?o Fadista
Ph.d. student
UNIVERSITY OF AARHUS
Faculty of Agricultural Sciences
Research Centre Foulum
Dept. of Genetics and Biotechnology
Blichers All? 20, P.O. BOX 50
DK-8830 Tjele
Phone: +45 8999 1900
Direct: +45 8999 1900
E-mail: Joao.Fadista at agrsci.dk
Web: http://www.agrsci.org
This email may contain information that is confidential.
Any use or publication of this email without written permission from
Faculty of Agricultural Sciences is not allowed.
If you are not the intended recipient, please notify Faculty of
Agricultural Sciences immediately and delete this email.
-----Original Message-----
From: J-C. Marioni [mailto:jcm68@hermes.cam.ac.uk]
Sent: Wednesday, February 07, 2007 11:28 AM
To: Jo?o 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, Jo?o 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
>
> Jo?o 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 All? 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=""/>
> ________________________________
>
> Tilmeld dig DJF's nyhedsbrev / Subscribe Faculty of Agricultural
Sciences Newsletter <http: www.agrsci.dk="" user="" register?lan="dan-DK"> .
>
> Denne email kan indeholde fortrolig information. Enhver brug eller
offentligg?relse af denne email uden skriftlig tilladelse fra DJF er
ikke tilladt. Hvis De ikke er den tilt?nkte adressat, bedes De
venligst straks underrette DJF samt slette emailen.
>
> This email may contain information that is confidential. Any use or
publication of this email without written permission from Faculty of
Agricultural Sciences is not allowed. If you are not the intended
recipient, please notify Faculty of Agricultural Sciences immediately
and delete this email.
>
>
>
> [[alternative HTML version deleted]]
>
>
