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 ??????????????? -------------------------------------------------- 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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.