[Bioc-devel] appropriate S4 class to contain microarray OR clinical feature data for clustering

Katie Planey katie.planey at gmail.com
Mon Mar 30 20:10:00 CEST 2015

Hi all,

I'm packaging my code for a meta-clustering method to submit to
Bioconductor, and I have the following design dilemma:  my method can be
used on either a matrix of gene expression data (well really any biological
data), or a matrix of clinical data. I would like to have the input data
matrices (one for each experiment) to be in standardized S4 objects, as
Bioconductor encourages.

But the eSet class is specifically designed for biological data. Is there a
broader S4 class I could use, or would I just instruct users with clinical
data to put their data matrix in the "featureData" slot? This clinical data
matrix would not contain outcomes variables; that could still potentially be
stored in the phenoData slot.  The AnnotatedDataFrame appears to  be too
simplistic, given that a user may still want to store several outcomes
variables in a phenoData or phenoData-like slot (varMetaData does from
AnnotatedDataFrame does not appear to fit this purpose).

Katie Planey
PhD Candidate | Stanford Biomedical Informatics

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