[Bioc-devel] RFC: eSet with two color data

"Simon Lin" <simonlin at duke.edu> writes:

I would also like to bring the attention to another single color platform, 
beadArray (by Illumina).

It sounds less complex (single color), but has more measurements (other than 
intensity) for each gene (more exactly, oligo reporter):
for example, number of beads, and standard deviation of on-the-array 
technical replicates.

We did model it in the lumi package, but we would certainly like to make the 
design more consistent with other packages.

I think that in the case of a BeadArraySet, that ExpressionSet is more
directly applicable.  If I understand your discription and based on
the code in the lumi package, you need more matrices conformant to
exprs but with different data, but don't have different phenoData for
each matrix type.

There is similar code in the beadarray package.  I would like to see
collaboration with Mark Dunning in any discussion of a more formal
BeadArraySet definition.


Best Wishes,

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org