[BioC] Writing own package description.

Sean Davis sdavis2 at mail.nih.gov
Wed Sep 7 16:09:04 CEST 2005

On 9/7/05 8:54 AM, "James W. MacDonald" <jmacdon at med.umich.edu> wrote:

> 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.

We also use custom arrays.  It suffices to write a little function to load
the data into the data structures provided by one of the "major players"
like limma or marray.  Then, all of the tools associated with those packages
are available.

The other package to look into, if you are really bioconductor-centric, is
AnnBuilder which allows you to build an annotation package for your array.


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