title: '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 positives, best previous method detected 72.6%. We also show that probes with differing binding affinity both hinder differential expression detection and introduce artifacts in cancer-healthy tissue comparison.
  
  
  CONCLUSIONS
  Detection and removal of such probes should be a routine step in Affymetrix data preprocessing. We prepared a user friendly R package, compatible with Bioconductor, that allows the filtering and improving of data from Affymetrix microarrays experiments.
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Dannemann
authors.forename: Michael
authors.initials: M
authors.lastname: Lachmann
authors.forename: Anna
authors.initials: A
authors.lastname: Lorenc
mesh_terms: D000818:Animals; D016477:Artifacts; D019295:Computational Biology / Q000379:methods; D001330:Electronic Data Processing / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation; D051379:Mice; D008810:Mice, Inbred C57BL; D008811:Mice, Inbred DBA; D015341:Nucleic Acid Probes / Q000302:isolation & purification*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software
chemical_list: D015341:Nucleic Acid Probes