I have a number of samples that have been profiled by different assays. For example, let's say 100 cell lines that have been assayed for the following features: gene expression (~20K genes), metabolism (1000 metabolites), and miRNA expression (>1000). I'd like to store these together in in a single S4 class object. eSets in Biobase seem to largely cover the need that I have, but the fact that I have a different number of features with different names means that the restriction on the assayData entries having the same dimensions prevents my usage eSet or one of its subclasses. Are there any other classes that would be more appropriate? Has anyone had to deal with this problem?
A group of us are in early stages of development of an object for the kind of application you're talking about. We have a prototype class at https://github.com/vjcitn/biocMultiAssay and would welcome your input in development or simply providing your use case or testing. I wouldn't yet recommend it for increasing your productivity, but for helping the group to design something that will meet your needs.