[BioC] simpleaffy problem with qc() applyed to an affybatch object from bovine

[James W. MacDonald]

D.Enrique ESCOBAR ESPINOZA wrote:
> no one gave me an answer to my problem posted last week,
> 
>>class(object)
> 
> [1] "AffyBatch"
> attr(,"package")
> [1] "affy"
> 
>>help(qc)
>>require(simpleaffy)
> 
> [1] TRUE
> 
>>require(bovinecdf)
> 
> [1] TRUE
> 
>>qc(object)
> 
> Background correcting
> Retrieving data from AffyBatch...done.
> Computing expression calls...
> ......done.
> scaling to a TGT of 100 ...
> Scale factor for: CG-13_faible-CCS.CEL 0.590320191208189
> Scale factor for: CG-30_faible-CCS.CEL 0.871856112275156
> Scale factor for: CG-48_forte-CCS.CEL 0.376163426955662
> Scale factor for: CG-65_forte-CCS.CEL 0.371390643693675
> Scale factor for: CG-84_forte-CCS.CEL 0.381544717241510
> Scale factor for: CG-87_faible-CCS.CEL 0.689233459604253
> Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about
> chip type: bovinecdf                   
> ???????????????

This means that there are no expected qc values for bovine chips in the 
simpleaffy package. You might try contacting Crispin Miller (the 
maintainer) directly to see if he can add that data for you. Otherwise, 
you will not be able to do the qc() stuff.

See packageDescription("simpleaffy")$M

HTH,

Jim


> 
> --------------------------------------------------
> D.Enrique ESCOBAR ESPINOZA
> (DESS Bioinfomatique
> B.Sc. Biologie Moleculaire
> Certificat Informatique) 
> http://adn.bioinfo.uqam.ca/~escd07097301/
> http://spaces.msn.com/members/escobarebio/
> ICQ#: 201778618
> -------------------------------------------------
> Tel: (514) 523-8398
> Montreal QC Canada
> 
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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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