[BioC] Writing own package description.

James W. MacDonald jmacdon at med.umich.edu
Wed Sep 7 14:54:15 CEST 2005

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.



> 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
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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