MAQC total RNA samples were processed following GE Healthcare's CodeLink(TM) iExpress Expression Assay Reagent Kit protocol (Please refer to CodeLink(TM) iExpress Expression Assay Regent Kit Technical Manual for details at www.codelinkbioarrays.com) and hybridized to CodeLink(TM) Human Whole Genome bioarrays (catalog #300026).
Scan protocol
All arrays were scanned on the GenePix 4000B scanner using manufacturer recommended settings of 600 PMT, 100% laser power, and 5 micron resolution.
Description
NA
Data processing
The resulting images were processed through the CodeLink Expression Analysis v4.1 software which automatically grids and quantifies each feature while assigning spot quality metrics. These quality metrics are applied to each spot and are displayed both numerically and as a qualitative assignment. In the MAQC study, for all microarray platforms, genes which were not detected (i.e., 'absent') were excluded from subsequent analyses. The spots which are below noise on the GE Healthcare platform are flagged by the software package as 'L' and represent cases where the spot mean intensity is less than local background median plus 1.5 standard deviations of local background. Details on the CodeLink(TM) detection algorithms can be found at the www.codelinkbioarrays.com (http://www1.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3AImproved+method%28275651129-B500%29?OpenDocument&hometitle=WebDocs).
Local background subtracted intensity data after median-scaling each array to a median of 1.
Flag_Detection
GEH's original flag information ('Quality_flag') is provided: G = 'Good', L = 'Absent', S = 'Saturated', M = 'Manufacturing Defect', I = 'Irregular Shape', C = 'Contaminated Spot'.