agilp

The current version contains a single function, AAProcess. AAProcess extracts the raw median signals from green and red channels of Agilent scanner array files. It replaces values for replicate probes by the mean of all replicates, and (optionally) removes control probes It log2 transforms data , and outputs txt files containing the red and green channel data separately. It then normalises each set of data against a baseline file (typically median or mean of a large set of arrays, using LOESS regression. Finally outputs the normalised data. The normalisation step can be optionally omitted.