[BioC] [Fwd: Bioc Book Chapter]

[Gordon K Smyth]

-------- Original Message --------
Subject: Bioc Book Chapter
From: "Rafael A. Irizarry" <ririzarr at jhsph.edu>
Date: Wed, January 28, 2004 7:43 am
To: Gordon Smyth <smyth at wehi.edu.au>

Dear Gordon,

The deadline for deciding on the bioc book chapter titles and authors is
fast approaching. As we discussed earlier, it seems two chapters could
be written for the chapter on cDNA (two color)
pre-processing. One about limma and one about marray*. I need to
decide on one. I've been looking at both packages closely and it seems
limma would be my choice.

It is likely that whatever package goes in this book will probably
become the "default" bioc package for two color preprocessing and it is
possible that the other would eventually be removed from
Bioconductor. However, I discussed this with other Bioconductor core
developers and some are concerned about limma not integrating well with
other Bioc packages. In particular Robert and others were hoping that
limma would use the exprSet class as its main data storage
entity. This would make data exchange to and from other packages much
easier. The exprSet class has recently been remodeled to better
reflect the needs of cDNA (two-color) arrays.  See
bioC/madman/Rpacks/Biobase/R/eset.R.

This is not a discussion for you and I to have but rather Bioconductor
as a whole. The main point is that if Bioconductor is willing to
accept limma as a default, and it appears the usage of exprSets will be
the requirement, I definetely would like to include a short chapter on
pre-processing cDNA arrays with limma as the package of
choice. Would you (or one of the grad students that helps you maintain
it) be willing to take the lead on such a chapter?

I am aware that the capabilities of limma extend far beyond
pre-processing. It is planned that the book will also contain "case
studies", from raw-data to result, and there, some of these further
capabilities should be demonstrated. But here, we are talking about
pre-processing.

If in fact we consolidate packages, for the users sake, the
functionality in marray that is not in limma (it does not appear to be
much) will need to be exported. I will also be contacting Jean who I
hope will be willing to collaborate with you in writing the chapter.

Best Regards,
Rafael