When I first started pulling GEO eSet representations into SE/sset objects,
I found that I had to write something to handle the mandatory MIAME data:
setAs("MIAME", "SimpleList",
function(from) { # {{{
to = list()
for(i in slotNames(from)) if(i != '.__classVersion__')
to[[i]]=slot(from, i)
return(SimpleList(to))
}
) # }}}
And then of course the SimpleList went into the sset exptData slot.
I've been doing this for a while to GEO data so that I can coerce it into
sset/SE objects (I'll start calling them 'sset' even though it doesn't make
sense as an acronym ;-)). But MIAME is, specifically, Minimal Information
About a Microarray Experiment. The closest I can think of would be the
MAGE-TAB representation for TCGA sequencing experiments. The
investigation (library prep, sequencing, quantification, etc.) is described
in the IDF:
https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thca/cgcc/unc.edu/illuminahiseq_rnaseqv2/rnaseqv2/unc.edu_THCA.IlluminaHiSeq_RNASeqV2.mage-tab.1.7.0/unc.edu_THCA.IlluminaHiSeq_RNASeqV2.1.7.0.idf.txt
The samples are then described in the SDRF:
https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thca/cgcc/unc.edu/illuminahiseq_rnaseqv2/rnaseqv2/unc.edu_THCA.IlluminaHiSeq_RNASeqV2.mage-tab.1.7.0/unc.edu_THCA.IlluminaHiSeq_RNASeqV2.1.7.0.sdrf.txt
And all the plain-English parts are further described here (thanks Katie!):
https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thca/cgcc/unc.edu/illuminahiseq_rnaseqv2/rnaseqv2/unc.edu_THCA.IlluminaHiSeq_RNASeqV2.mage-tab.1.7.0/DESCRIPTION.txt
Speaking from experience, it is a pain in the (arbitrary appendage) to
assemble these, but they are essentially self-contained experiments for the
end user. This is one of the reasons I like using sset objects even for
data from GEO: I can keep all the exptData, I can map all the
probes/reads/etc. to the appropriate genome build (and swap/lift assemblies
as needed), and it's trivial to compare (say) RNAseq results to HuEx to 3'
array results.
So I'm not against support for this, although it would make rival labs'
lives easier, which isn't always my goal in life ;-)
On Sun, Feb 3, 2013 at 9:32 AM, Martin Morgan <mtmor...@fhcrc.org> wrote:
> 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__"
>
> Martin
>
>
>
>> best,
>>
>> Mike
>>
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>>
>
>
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> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
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>
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>
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*A model is a lie that helps you see the truth.*
*
*
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