benilton/pdInfoBuilder — pull request #4 by jmacdon (2014-11-21 22:13:35+00:00)
Title: Changes to accommodate Mouse Transcriptome 1.0 arrays

This is the same as for the release version:

Affy has added three new types of 'main' probes, main->junctions, main->psrs, and main->rescue. I added these to getTypeSchema().

They also have probesets (PSR and JUC) on the Mouse Transcriptome 1.0 array that are in the design (and so are in the probeset and transcript csv files), but that are not actually on the array, either because the sequences were too repetitive to synthesize the probes, or that were junction probes that were either too short, or that extended past the region they were supposed to measure.

Regardless, these phantom probesets muck things up because when we create the featureSet, it ends up with 811 probesets (meta_fsetid)s that don't have an associated fsetid (it's an NA), which causes problems when the featureSet data.frame is dropped into the db table, because the fsetids are all supposed to be unique, so 811 NAs is a problem. I just remove the phantom meta_fsetids from the probesetInfo[["probesets"]] data.frame.