A new method for class prediction based on signed-rank algorithms applied to Affymetrix microarray experiments

BMC Bioinformatics
Thierry RemeBernard Klein

Abstract

The huge amount of data generated by DNA chips is a powerful basis to classify various pathologies. However, constant evolution of microarray technology makes it difficult to mix data from different chip types for class prediction of limited sample populations. Affymetrix(R) technology provides both a quantitative fluorescence signal and a decision (detection call: absent or present) based on signed-rank algorithms applied to several hybridization repeats of each gene, with a per-chip normalization. We developed a new prediction method for class belonging based on the detection call only from recent Affymetrix chip type. Biological data were obtained by hybridization on U133A, U133B and U133Plus 2.0 microarrays of purified normal B cells and cells from three independent groups of multiple myeloma (MM) patients. After a call-based data reduction step to filter out non class-discriminative probe sets, the gene list obtained was reduced to a predictor with correction for multiple testing by iterative deletion of probe sets that sequentially improve inter-class comparisons and their significance. The error rate of the method was determined using leave-one-out and 5-fold cross-validation. It was successfully applied to (i) determine...Continue Reading

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Citations

Nov 27, 2009·Briefings in Bioinformatics·Kellie J Archer, Sarah E Reese
Jan 30, 2009·Bioinformatics·Thomas LaFramboiseRoman K Thomas
Nov 13, 2012·Biochemical and Biophysical Research Communications·Jerome MoreauxBernard Klein
Mar 10, 2009·Biochemical and Biophysical Research Communications·Matthieu SchoenhalsBernard Klein
Feb 3, 2009·British Journal of Haematology·Michel JourdanBernard Klein
Sep 16, 2011·The Journal of Immunology : Official Journal of the American Association of Immunologists·Michel JourdanBernard Klein
Jun 29, 2012·Cancer Research·Sylvanie SurgetCatherine Pellat-Deceunynck

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Methods Mentioned

BETA
chip
chips

Software Mentioned

Prediction Analysis of Microarrays ( PAM
PAM
RAGE
Affymetrix
GCOS
PAN
MAS5
Perl
Linux
CGI scripts

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