[BioC] Create A Stranded probeAnno Object

[Dario Strbenac]

Also worth describing in ?probeAnno

> probes
Error in validObject(object) : 
  invalid class “probeAnno” object: 1: Probe matches are not sorted (in 
increasing order) by their middle position on chromosome chr1.- and possibly 
others.

invalid class “probeAnno” object: 2: Probe matches are not sorted (in 
increasing order) by their middle position on chromosome chr1.+ and possibly 
others.

invalid class “probeAnno” object: 3: Probe matches are not sorted (in 
increasing order) by their middle position on chromosome chr10.- and possibly 
others.
...                                ...

Also, I need to write a workaround for segChrom for any chromosomes that don't 
have probes on both strands (boutique design array).

...                                ...
Running 'segment' on chromosome chr12.+ ... complete
Running 'segment' on chromosome chr12.- ... complete
Running 'segment' on chromosome chr13.+Error in probeAnno[w] : 
  No mapping 'chr13.+.start' in this 'probeAnno' object.

> probes
A 'probeAnno' object holding the mapping between
reporters and genomic positions.
Chromosomes: chr1.- chr1.+ chr10.- chr10.+ chr11.- chr11.+ chr12.- chr12.+ 
chr14.- chr14.+ chr15.- chr15.+ chr16.- chr16.+ chr17.- chr17.+ chr18.- chr18.+ 
chr19.- chr19.+ chr2.- chr2.+ chr20.- chr20.+ chr21.- chr21.+ chr22.- chr22.+ 
chr3.- chr3.+ chr4.- chr4.+ chr5.- chr5.+ chr6.- chr6.+ chr7.- chr7.+ chr8.- 
chr8.+ chr9.- chr9.+ chrX.- chrX.+ chrY.- chrY.+
Microarray platform:  
Genome: 

Gives a valid object, so segChrom should work with it.

- Dario