Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis – Protocol (AG1). These protocols are available for download at http://www.chem.agilent.com/scripts/generic.asp?lpage=11617&indcol=N&prodcol=Y. The microarrays used were Agilent’s Whole Human Genome Oligo Microarrays (P/N G4112A). Probe sequence information is publicly available at http://www.chem.agilent.com/cag/bsp/bsp_register.asp. Labeled cRNAs were generated from 500 ng of total RNA for each of AG1 and AGL using Agilent’s Low RNA Input Linear Amplification Kit (P/N 5188-5339). Agilent’s Stabilization and Drying Solution was used in processing all microarrays.
Scan protocol
Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA) and data extracted using Agilent's Feature Extraction software, version 8.5 (P/N G2567AA). AG1 data were processed using Agilent’s GeneSpring® GX software, version 7.3 (P/N G1745).
Description
NA
Data processing
Data were transformed by setting all measurements less than 5.0 to 5.0. Data points that did not have detectable signal and those that represent microarray controls were labeled as Absent, those representing either non-uniform or saturated features were labeled as Marginal, and all remaining data points were labeled as Present. All data points were median scaled using the median signal intensity value for data points labeled as Present.
Local background subtracted intensity data after median-scaling each array (Present only) to a median of 1.
Flag_Detection
Data points that did not have detectable signal and those that represent microarray controls were labeled as Absent, those representing either non-uniform or saturated features were labeled as Marginal, and all remaining data points were labeled as Present.
