Inverse Langmuir method for oligonucleotide microarray analysis.

ABSTRACT:

Background

An algorithm for the analysis of Affymetrix Genechips is presented. This algorithm, referred to as the Inverse Langmuir Method (ILM), estimates the binding of transcripts to complementary probes using DNA/RNA hybridization free energies, and the hybridization between partially complementary transcripts in solution using RNA/RNA free energies. The balance between these two competing reactions allows for the translation of background-subtracted intensities into transcript concentrations.

Results

To validate the ILM, it is applied to publicly available microarray data from a multi-lab comparison study. Here, microarray experiments are performed on samples which deviate only in few genes. The log2 fold change between these two samples, as obtained from RT-PCR experime

SUBMITTER: Mulders GC 

PROVIDER: S-EPMC2661052 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature