[Bioc-devel] Biobase eSet and exprSet validation

[Martin Morgan]

Bioconductors,

A recent change to Biobase checks that eSet and exprSet objects have
the correct format, and in particular that the 'sampleNames' are
identical to the row names of the phenoData. This consistency is
important, because it is what allows coordination between the
expression and phenotype data.

The change creates a certain amount of havoc with other
packages. Often the consequences are minor (e.g., creating an invalid
object in a vignette), but it would be great to have these cleaned up
in the next couple of weeks. Please let me or the list know if we can
help, or if the object validation needs tweaking.

Now might also be a good time to replace any use of the deprecated
eset data with the new sample.eSet and sample.exprSet data sets.

Errors during build (e.g.,  functions constructing invalid objects)

GEOquery
LMGene
affycoretools
ecolitk
matchprobes
metaArray
sscore

Errors during check (e.g., examples, vignettes)

MergeMaid
affy
convert
edd
macat

Cheers!
-- 
Martin Morgan