1. Dictionary: 1. Dictionary
Description
This part describes non-obvious terms used in this package.
- affxparser
- The name of this package.
APIApplication program interface, which describes the
functional interface of underlying methods.
block(aka group).
BPMAPA file format containing information
related to the design of the tiling arrays.
CalvinA special binary file format.
CDFA file format: chip definition file.
CELA file format: cell intensity file.
cell(aka feature) A probe.
cell indexAn integer that identifies a probe uniquely.
chipAn array.
chip typeAn identifier specifying a chip design
uniquely, e.g. "Mapping50K_Xba240"
.
DATA file format: contains pixel intensity
values collected from an Affymetrix GeneArray scanner.
featureA probe.
Fusion SDKOpen-source sofware development kit (SDK) provided
by Affymetrix to access their data files.
group(aka block)
Defines a unique subset of the cells in a unit.
Expression arrays typically only have one group per unit, whereas
SNP arrays have either two or four groups per unit, one for each of
the two allele times possibly repeated for both strands.
MMMismatch-match, e.g. MM probe.
PGFA file format: probe group file.
TPMAPA file format storing the relationship between (PM,MM)
pairs (or PM probes) and positions on a set of sequences.
QCQuality control, e.g. QC probes and QC probe sets.
unitA probeset.
XDAA file format, aka as the binary file format.