[Bioc-devel] Multiple colData in SummarizedExperiment

davide risso risso.davide at gmail.com
Wed Jun 17 20:41:26 CEST 2015

Dear list,

I'm creating an R package to store RNA-seq data of a somewhat large project
in which I'm involved.

One of the initial goals is to compare different pre-processing pipelines,
hence I have multiple expression matrices corresponding to the same samples.
The SummarizedExperiment class seems a good candidate, since I have
multiple expression matrices with the same rowData and colData information.

I have several sample-specific variables that I want to store with the
object, namely, experimental information (e.g., batch, date, experimental
condition, ...) and sample quality (e.g., proportion of aligned reads,
total duplicate reads, etc...).

Of course, I can always create one big data frame concatenating the two
(experimental info + sample quality), but it seems that both conceptually
and practically, it might be useful to have two separate data frames.
Since this seems somewhat a reasonably standard type of information that
one would want to carry on, I was wondering if it would be possible /
useful to allow the user to have multiple data.frames in the colData slot
of SummarizedExperiment.


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