Microarray Data Processing: Agilent
Raw dataQuantified image data is generated by the Agilent Feature Extraction Software with default options.
Background Correction and Normalization
B-Fabric applications start from the raw data produced by the Agilent Feature Extraction Software. The raw files contain different values, that values that are used are indicated by the parameter Data Used:
- gMedianSignal: the median spot intensities without background correction
- gProcessedSignal: the median spot intensities with background correction and spatial detrending
For normalization B-Fabric uses by default the quantile normalization implemented in the Bioconductor package preprocessCore.
Please see the Two Groups Analysis (Microarray) page.