From hybridization theory to microarray data analysis: performance evaluation.

ABSTRACT:

Background

Several preprocessing methods are available for the analysis of Affymetrix Genechips arrays. The most popular algorithms analyze the measured fluorescence intensities with statistical methods. Here we focus on a novel algorithm, AffyILM, available from Bioconductor, which relies on inputs from hybridization thermodynamics and uses an extended Langmuir isotherm model to compute transcript concentrations. These concentrations are then employed in the statistical analysis. We compared the performance of AffyILM and other traditional methods both in the old and in the newest generation of GeneChips.

Results

Tissue mixture and Latin Square datasets (provided by Affymetrix) were used to assess the performances of the differential expression analysis depending on the pre

SUBMITTER: Berger F 

PROVIDER: S-EPMC3267830 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature