'maskBAD'--a package to detect and remove Affymetrix probes with binding affinity differences.

ABSTRACT:

Background

Hybridization differences caused by target sequence differences can be a confounding factor in analyzing gene expression on microarrays, lead to false positives and reduce power to detect real expression differences. We prepared an R Bioconductor compatible package to detect, characterize and remove such probes in Affymetrix 3'IVT and exon-based arrays on the basis of correlation of signal intensities from probes within probe sets.

Results

Using completely mouse genomes we determined type 1 (false negatives) and type 2 (false positives) errors with high accuracy and we show that our method routinely outperforms previous methods. When detecting 76.2% of known SNP/indels in mouse expression data, we obtain at most 5.5% false positives. At the same level of false pos

SUBMITTER: Dannemann M 

PROVIDER: S-EPMC3439685 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature