Microarray Data Processing: Agilent

Raw data

Quantified 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.

Differential Expression

Please see the Two Groups Analysis (Microarray) page.