snapCGH - subscript out of bounds
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João Fadista ▴ 500
@joao-fadista-1942
Last seen 9.6 years ago
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J-C. Marioni ▴ 40
@j-c-marioni-2033
Last seen 9.6 years ago
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]] > >
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João Fadista ▴ 500
@joao-fadista-1942
Last seen 9.6 years ago
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]] > >
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