Hi, i've learn through the many tutorials and courses available on the net (thanks to everybody for that, it's wonderfull), and i really like working with bioc. I work in a lab where we use a cDNA, home made chip. I was wondering how i could write a package for R to describe this particular chip, and use all the possibility of bioconductor with it, because all that i learned with tutorials was with affy chips. I've read some documents but i'm still a bit confused about that. The exprset structure is for data, isn't it ? So in it, i'll put results from my experiments, and also phenoData. But i also need to describe which probe correspond to which gene ? no ? How could i start ? thanks for your answers. Julien Textoris

TEXTORIS Julien wrote: > Hi, > > i've learn through the many tutorials and courses available on the net > (thanks to everybody for that, it's wonderfull), and i really like > working with bioc. > > I work in a lab where we use a cDNA, home made chip. I was wondering how > i could write a package for R to describe this particular chip, and use > all the possibility of bioconductor with it, because all that i learned > with tutorials was with affy chips. I am not sure you need to write a package for any of this. There are already packages in BioC that are designed to normalize (marray, limma) and make comparisons (limma, multtest, factDesign) using cDNA arrays. I suppose there may be some functionality you might like that is not implemented in these packages, but I would recommend starting with the existing packages. IIRC, all of these packages have vignettes, so that would probably be the best place to start. Best, Jim > > I've read some documents but i'm still a bit confused about that. > The exprset structure is for data, isn't it ? So in it, i'll put results > from my experiments, and also phenoData. But i also need to describe > which probe correspond to which gene ? no ? > > > How could i start ? > > thanks for your answers. > > Julien Textoris > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald 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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