Status: Archived project, active between 2007 and 2016
Calibration of microarray measurements aims at removing systematic biases from the probe-level data to get expression estimates which linearly correlate with the transcript abundance in the studied samples. We address hybridization on microarrays as a reaction process in a complex environment and express the measured intensities as a function of the input quantities of the experiment.
The hook-method is a calibration approach which is based on a graphical summary of the actual hybridization characteristics of a particular microarray. The hook method provides a set of chip summary characteristics which evaluate the performance of a given hybridization. The theory and algorithm of the method is described in this paper.
The C++ implementation "Larpack" includes the most recent procedures producing most robust results.
The correction of CEL-files for the effect of G-stacks (described in the BMC Bioinformatics publication) is implemented in Larpack. Please use arrayCorrect with the command-line option "--update-celfiles".
This repository contains Revision 493 of the original SVN repository (from Jun 2010). The source code contains contains arrayCorrect, pmOnlyCorrect, correctCelfile and the R Package. The windows binary arrayCorrect is available upon request, or can be build using the instructions in the repository (needs the Visual C++ Redistributable).
Please find further publications regarding Larpack analysis here