Algorithm Output Definitions for Affymetrix GeneChip expression analysis

Signal:  A measure of the abundance of a transcript.

Stat Pairs:  The number of probes pairs for a particular probe set on the array.

Stat Pairs Used:  =Pairs-Masked probe pairs-Saturated MM probe pairs.  This is the number of pairs used by the Statistical Expression algorithm to make the detection call in an absolute analysis.

Detection:  The call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M) or no call (NC).

Detection P-value:  p-value that indicates the significance level of the detection call.

Stat Common Pairs:  The intersection of the probe pairs from the baseline and experiment that are used by the Statistical Expression algorithm to make the change call in a comparison analysis.

Change:  The call that indicates the change in transcript level between a baseline and an experiment array.

Change p-value:  p-value indicates the significance level of the change call.

Signal log ratio:  The change in expression level for a transcript between a baseline and an experiment array.  This change is expressed as the log₂ ratio. 

Signal log ratio low:  The lower limit of the log ratio within a 95% confidence range.

Signal log ratio high:  The upper limit of the signal log ratio within a 95% confidence range.

Terms for Affymetrix GeneChip expression analysis

Target: The target is the biotin-labeled RNA that is being hybridized to the probe array. 

Probe: A single stranded DNA oligonucleotide (25-mer) on the array that is complementary to a specific sequence.

Probes:  The oligonucleotides on the surface of the probe arrays are called probes because they probe or interrogate the sample.

Probe cell:  A single square-shaped area on the array that contains many copies of a given 25-mer oligonucleotide or probe. 

Perfect Match (PM): The sequence of PM is complementary to a specific sequence.

Mismatch (MM): The sequence of MM is same as PM except for a base substitution in the middle of the MM probe sequence. 

Probe Pair: (PM) Perfect Match probe and (MM) Mismatch probe.

Probe Set:  A probe set includes a series of probe pairs and represents and expressed transcript.

Absolute Expression Analysis:  An absolute expression analysis examines the cell intensity file (*.CEL) from one experiment (Single GeneChip probe array). 

Comparison Expression Analysis:  Comparison analysis compares the cell intensities of the same probe set on two different probe arrays (an experiment and baseline of the same probe array type) to determine the relative change in the expression level of a transcript.