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LIFE - Transcriptomics Group

Bioinformatik Uni Leipzig

http://www.life.uni-leipzig.de

Hook analysis of GeneChip microarrays

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 new 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.

There are two implementations of the hook method. The C++ implementation includes the most recent procedures producing more robust results. The Java implementation is not updated anymore but easily runs on any system with a Java Runtime Environment.

News: The correction of CEL-files for the effect of G-stacks (described in the recent BMC Bioinformatics publication) is implemented in the Larpack. Please use arrayCorrect with the command-line option "--update-celfiles".

Larpack (C++/R implementation)
  • Source Code [tar.gz, 220KB, Revision 493: Jun 2010] (contains arrayCorrect, pmOnlyCorrect, correctCelfile and R Package)
  • Windows-Binary arrayCorrect [ZIP, 1MB, Revision 482: Dec 2009] (needs the Visual C++ Redistributable)
  • Short Installation Guide [PDF / HTML]
  • Manpage describing program options [HTML]


Hook-program (Java implementation)
  • Hook-program v1.01 (16 MB, version with example) [zip]
  • Short installation guide [PDF]
  • Hook paper [PDF]
  • FAQs and Bugs [PDF / HTML]


Please mail your experiences and possible problems.

Quality reports:


Contact:
  • Hans Binder
  • Stephan Preibisch
  • Jan Brücker
  • Mario Fasold


Further paper on microarray analysis:
Binder H, Krohn K, Preibisch S.
"Hook" calibration of GeneChip-microarrays: chip characteristics and expression measures.
Algorithms for Molecular Biology 2008; 3:11
PDF | Publisher's page
Binder H, Preibisch S.
"Hook" calibration of GeneChip-microarrays: Theory and algorithm.
Algorithms for Molecular Biology 2008; 3:12
PDF | Publisher's page
Binder, H.
Thermodynamics of competitive surface adsorption on DNA-microarrays.
J. Phys. Cond. Matter 18: 491-523 (2006).
PDF
Binder, H., Preibisch, S.
GeneChip microarrays - signal intensities, RNA-concentrations and probe sequences.
J. Phys. Cond. Matter 18: 537-566 (2006).
PDF
Binder, H.
Probing gene expression - sequence specific hybridization on microarrays.
In: Bioinformatics of Genome Regulation and Structure II (Eds. N. Kolchanov and R. Hofestaedt (Eds.), Springer Science+Business Media, Inc. 2005, pp. 451-466.
PDF
Binder, H., Preibisch, S., Kirsten, T.
Base pair interactions and hybridization isotherms of matched and mismatched oglionucleotide probes on microarrays.
Langmuir 2005, 21, 9287-9302.
PDF, Supporting information
Binder, H., Preibisch, S.
Specific and non specific hybridization of oglionucleotide probes on microarrays.
Biophys. J., 2005. 89: 337-352.
PDF
Binder, H., Kirsten, T., Hofacker, I.L., Stadler, P.F., Loeffler, M.
Interactions in oligonucleotide hybrid duplexes on microarrays.
J. Phys. Chem. B , 2004. 108 (46): p. 18015-18025
PDF
Binder, H., Kirsten, T., Loeffler, M., Stadler, P.F.
The sensitivity of microarray oligonucleotide probes - variability and the effect of base composition.
J. Phys. Chem. B , 2004. 108 (46): p. 18003-18014
PDF