[Bioc-devel] Subsetting affybatch and exprset objects

Rafael A. Irizarry ririzarr at jhsph.edu
Fri Apr 30 04:47:06 CEST 2004

ive just made this change (not commited yet). however, instead of an error
im giving a "decrepit" warning cause i suspect many people use abatch[1]
(since its in the vignette). in the next release ill make it an error.

abatch[,j] now does waht is expected.

On Tue, 13 Apr 2004, Vincent Carey 525-2265 wrote:

> > the problem is th if you subset eset by the first dimension then you
> > loose the position structure, and as a consequence the locations of pms
> > and mms held in the cdfenv are no longer meaningful. if there are any
> > suggestions on what eset[i,] should return id be happy to consider them.
> at this time i would suggest for an AffyBatch eset: eset[i,] should fail
> with a notice that subsetting by probe is not supported; eset[,j] should
> succeed as it keeps the analogy to exprSet indexing; and eset[j] should
> fail with wrong number of dimensions.
> i think that comma-less subscripting of exprSets should fail too -- but
> currently if eset is an exprSet, eset[j] corresponds to gene-level
> subsetting.  do we really need that?

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