I am using the oligo package in R for bioinformatics analysis. I am analysising data produced using the rat exon array GeneChip® Rat Exon 1.0 ST Array
I was wondering about the summarisation of probesets at the gene level, particularly for the exon arrays, but this would apply to the ST arrays too.
When summarising at the gene level with the oligo package, I understand it summarises all probesets that map to the exons of a given gene.
Is any distinction made beween probesets that map to exons that are always expressed in all splice variants of a given gene, and exons that are sometimes included, sometimes not?
Obviously for exons that are not always included, given that they will be given a background intensity value, if they make up more than 50% of the exons of a gene, this could lead to problems later on; expression would be greatly underestimated.