Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays.
Probe defects are a major source of noise in gene expression studies. While existing approaches detect noisy probes based on external information such as genomic alignments, we introduce and validate a targeted probabilistic method for analyzing probe reliability directly from expression data and independently of the noise source. This provides insights into the various sources of probe-level noise and gives tools to guide probe design.
Helsinki Institute for Information Technology, Department of Information and Computer Science, Aalto University School of Science and Technology, PO Box 15400, FI-00076 Aalto, Finland. leo.lahti@iki.fi
Leo
L
Lahti
Laura L
LL
Elo
Tero
T
Aittokallio
Samuel
S
Kaski
D000465:Algorithms; D016009:Chi-Square Distribution; D019295:Computational Biology / Q000592:standards*; D020869:Gene Expression Profiling / Q000592:standards*; D016678:Genome; D006801:Humans; D015233:Models, Statistical; D016011:Normal Distribution; D015341:Nucleic Acid Probes / Q000592:standards*; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D020641:Polymorphism, Single Nucleotide; D012372:ROC Curve; D015203:Reproducibility of Results; D016415:Sequence Alignment
D015341:Nucleic Acid Probes