STATISTICAL ALGORITHM OUTPUT DEFINITIONS

Versions of Microarray Suite software 5.0 and above, inlcuding the GeneChip Operating Software (GCOS) run the statistical algorithm. The following descriptions of column headers were obtained from Affymetrix (http://www.affymetrix.com).


SINGLE-ARRAY RESULTS


Signal: 
-------
A measure of the abundance of a transcript.


Detection: 
----------
The call that indicates whether the transcript is detected (P, Present), undetected (A, Absent), or at the limit of detection (M, Marginal). 


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


Stat Pairs: 
-----------
The number of probe pairs for a particular probe set on an array.


Stat Pairs Used:
----------------
The number of probe pairs per probe set used in the analysis.  This may be the total number of probes per probe set on the probe array or the number of probe pairs in a pre-designated subset (for example, probe pairs specified by a probe mask file and/or masked image).  

Stat Pairs Used = total probe pairs per probe set - (probe pairs masked in a mask file) - (probe pairs masked in the image) - (Saturated MM probe pairs)



COMPARISON RESULTS


Signal Log Ratio: 
-----------------
The change in the expression level of a transcript between a baseline and an experiment array. This change is expressed as the log2 ratio.  A log2 ratio of 1 is equal to a fold change of 2.


Signal Log Ratio low: 
--------------------
The lower limit of the Log Ratio within a 95% confidence interval.


Signal Log Ratio high: 
---------------------
The upper limit of the Signal Log Ratio within a 95% confidence interval.

Change: 
-------
The call that indicates the change in the transcript level between a baseline and an experiment (Increase (I), Marginal Increase (MI), No Change (NC), Marginal Decrease (MD), Decrease (D)).


Change p-value: 
---------------
p-value that indicates the significance of the Change 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.