[Bioc-devel] information about sequencing experiment

Martin Morgan mtmorgan at fhcrc.org
Sun Feb 3 18:32:35 CET 2013

On 02/03/2013 06:37 AM, Mike Love wrote:
> hi,
> Does/should there exist a class similar to MIAME for sequencing data, e.g. slots
> concerning the library preparation, alignment, etc.?
> This could then be suggested as something to include in the exptData SimpleList
> of SummarizedExperiment.

As it is one could certainly

 > se = SummarizedExperiment()
 > exptData(se) = list(MIAME())

If we want to go down this route then I think the right strategy would be to 
make the exptData slot more strict. But what would the MIAME-like container look 
like? The basics are probably shared, but what else?

 > slotNames("MIAME")
  [1] "name"              "lab"               "contact"
  [4] "title"             "abstract"          "url"
  [7] "pubMedIds"         "samples"           "hybridizations"
[10] "normControls"      "preprocessing"     "other"
[13] ".__classVersion__"


> best,
> Mike
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