This part describes non-obvious terms used in this package. affxparser The name of this package. API Application program interface, which describes the functional interface of underlying methods. block (aka group). BPMAP A file format containing information related to the design of the tiling arrays. Calvin A special binary file format. CDF A file format: chip definition file. CEL A file format: cell intensity file. cell (aka feature) A probe. cell index An integer that identifies a probe uniquely. chip An array. chip type An identifier specifying a chip design uniquely, e.g. "Mapping50K_Xba240". DAT A file format: contains pixel intensity values collected from an Affymetrix GeneArray scanner. feature A probe. Fusion SDK Open-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. MM Mismatch-match, e.g. MM probe. TPMAP A file format storing the relationship between (PM,MM) pairs (or PM probes) and positions on a set of sequences. QC Quality control, e.g. QC probes and QC probe sets. unit A probeset. XDA A file format, aka as the binary file format. 1 2 2. Cell coordinates and cell indices Author(s
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