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'maskBAD' - a package to detect and remove Affymetrix probes with binding affinity differences
- Source :
- BMC Bioinformatics, BMC Bioinformatics, Vol 13, Iss 1, p 56 (2012)
- Publisher :
- Springer Nature
-
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.
- Subjects :
- Electronic Data Processing
Gene Expression Profiling
Computational Biology
lcsh:Computer applications to medicine. Medical informatics
Polymorphism, Single Nucleotide
Biochemistry
Computer Science Applications
Mice, Inbred C57BL
Mice
Nucleic Acid Probes
lcsh:Biology (General)
INDEL Mutation
Mice, Inbred DBA
lcsh:R858-859.7
Animals
Humans
Artifacts
lcsh:QH301-705.5
Molecular Biology
Software
Oligonucleotide Array Sequence Analysis
Subjects
Details
- Language :
- English
- ISSN :
- 14712105
- Volume :
- 13
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- BMC Bioinformatics
- Accession number :
- edsair.pmid.dedup....ddd5d8612c5f3f827cfe43265a5ca5cc
- Full Text :
- https://doi.org/10.1186/1471-2105-13-56