Clinically validated benchmarking of normalisation techniques for two-colour oligonucleotide spotted microarray slides.
Acquisition of microarray data is prone to systematic errors. A correction, called normalisation, must be applied to the data before further analysis is performed. With many normalisation techniques published and in use, the best way of executing this correction remains an open question. In this study, a variety of single-slide normalisation techniques, and different parameter settings for these techniques, were compared over many replicated microarray experiments. Different normalisation techniques were assessed through the distribution of the standard deviation of replicates from one biological sample across different slides. It is shown that local normalisation outperformed global normalisation, and intensity-based 'LOWESS' outperformed trimmed mean and median normalisation techniques. Overall, the top performing normalisation technique was a print-tip-based LOWESS with zero robust iterations. Lastly, we validated this evaluation methodology by examining the ability to predict oestrogen receptor-positive and -negative breast cancer samples with data that had been normalised using different techniques.
Listgarten
Jennifer
J
PolyomX Program, Cross Cancer Institute, University of Alberta, Alberta Cancer Board, Edmonton, AB, Canada. jenn@cs.toronto.ca
Graham
Kathryn
K
Damaraju
Sambasivarao
S
Cass
Carol
C
Mackey
John
J
Zanke
Brent
B
D000465:Algorithms; D019985:Benchmarking / Q000379:methods*; D014408:Biomarkers, Tumor / Q000235:genetics; D001943:Breast Neoplasms / Q000235:genetics; D002138:Calibration / Q000592:standards; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods* / Q000592:standards*; D005820:Genetic Testing / Q000379:methods; D006801:Humans; D036641:Microscopy, Fluorescence, Multiphoton / Q000295:instrumentation / Q000379:methods / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods* / Q000592:standards*; D011786:Quality Control; D011960:Receptors, Estrogen / Q000235:genetics; D012015:Reference Standards; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D013050:Spectrometry, Fluorescence / Q000295:instrumentation / Q000379:methods / Q000592:standards
D014408:Biomarkers, Tumor; D011960:Receptors, Estrogen