[Bioc-devel] oligo package, SNP+expr data

Benilton Carvalho bcarvalh at jhsph.edu
Tue Feb 6 19:41:52 CET 2007

Hi Jeff,

> To get the ball rolling, I took a look at the oligo package to get  
> a sense
> for what containers it currently had, and how they worked.  There were
> four in particular that caught my eye:
> - The SnpCallSet:  Looks to essentially be an eSet object, but
> replacing the expression matrix with a matrix of the calls

the SnpCallSet also has a container for the confidence associated to  
the call.

> - The SnpCopyNumberSet: Same, but with copy #

Same as above (a container for confidence)

> - oligoSnpSet: A container which would hold both calls & copy #  
> (correct?)


> - SnpQSet: This I'm not sure what it represents, but is the output  
> of the
> snprma() functionality

The SnpQSet (the "Q" stands for "quantification") contains the  
summaries for the SNPs. The approach that we use summarizes each  
featureset to 4 numbers (alleles A and B / strands sense and antisense).

Does that help you?


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