geoscience.net logo
+ Resolve Article
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter

+ Translate
+ Subscribe to Site Feed
GeoScience Most Shared ContentMost Shared Content

An interactive power analysis tool for microarray hypothesis testing and generation


, : An interactive power analysis tool for microarray hypothesis testing and generation. Bioinformatics 22(7): 808-814

Motivation: Human clinical projects typically require a priori statistical power analyses. Towards this end, we sought to build a flexible and interactive power analysis tool for microarray studies integrated into our public domain HCE 3.5 software package. We then sought to determine if probe set algorithms or organism type strongly influenced power analysis results.Results: The HCE 3.5 power analysis tool was designed to import any pre-existing Affymetrix microarray project, and interactively test the effects of user-defined definitions of alpha (significance), beta (1 - power), sample size and effect size. The tool generates a filter for all probe sets or more focused ontology-based subsets, with or without noise filters that can be used to limit analyses of a future project to appropriately powered probe sets. We studied projects from three organisms (Arabidopsis, rat, human), and three probe set algorithms (MAS5.0, RMA, dChip PM/MM). We found large differences in power results based on probe set algorithm selection and noise filters. RMA provided high sensitivity for low numbers of arrays, but this came at a cost of high false positive results (24% false positive in the human project studied). Our data suggest that a priori power calculations are important for both experimental design in hypothesis testing and hypothesis generation, as well as for the selection of optimized data analysis parameters.

US$19.90

PMID: 16418236

DOI: 10.1093/bioinformatics/btk052


Other references

Christen, K., 2006: Bottled antimony. Environmental Science & Technology 40(8): 2500-2501

Maupin, C.Mark.; Castillo, N.; Taraphder, S.; Tu, C.; McKenna, R.; Silverman, D.N.; Voth, G.A., 2011: Chemical rescue of enzymes: proton transfer in mutants of human carbonic anhydrase II. In human carbonic anhydrase II (HCA II), the mutation of position 64 from histidine to alanine (H64A) disrupts the rate limiting proton transfer (PT) event, resulting in a reduction of the catalytic activity of the enzyme as compared to the wild-t...

IIda J.; Miura F., 1982: Fundamental research of chemical mediators during experimental tooth movement 1. Journal of Dental Research 61(4): 597

Zmijewski, C.M.; Engel, E.; Croce, C.M., 1978: Expression of HLA-A, but not of HLA-B, in mouse-human somatic cell hybrids carrying the region p21 leads to pter of human chromosome 6. Mouse-human somatic cell hybrids containing human chromosome 17 carrying the region p21 leads to pter of human chromosome 6 and no other human chromosomes, were found to express HLA-A but not HLA-B. Counterselection of the hybrid cells in medium c...

Renner, M.C.; Albers, E.Hh.; Gutierrez-Castellanos, N.; Reinders, N.R.; van Huijstee, A.N.; Xiong, H.; Lodder, T.R.; Kessels, H.W., 2017: Synaptic plasticity through activation of GluA3-containing AMPA-receptors. Excitatory synaptic transmission is mediated by AMPA-type glutamate receptors (AMPARs). In CA1 pyramidal neurons of the hippocampus two types of AMPARs predominate: those that contain subunits GluA1 and GluA2 (GluA1/2), and those that contain GluA...

Smichi, N.; Fendri, A.; Zarai, Z.; Bouchaala, E.; Chérif, S.; Gargouri, Y.; Miled, N., 2013: Lipolytic activity levels and colipase presence in digestive glands of some marine animals. Studies on the digestive secretions in aquatic animals can elucidate certain aspects of their nutritive physiology. The aim of the present study was to compare the digestive lipase and phospholipase activities in ten marine species belonging to fo...

Stasiolek, M.; Linker, R.A.; Hayardeny, L.; Bar Ilan, O.; Gold, R., 2015: Immune parameters of patients treated with laquinimod, a novel oral therapy for the treatment of multiple sclerosis: results from a double-blind placebo-controlled study. Laquinimod is a novel orally administered drug for the treatment of relapsing remitting multiple sclerosis (RRMS). In this immunological substudy of the phase III Assessment of Oral Laquinimod in Preventing Progression of MS (ALLEGRO) trial, we pe...

Miller, J., 2015: ASAM criteria becomes electronic tool. Behavioral Healthcare 35(1): 25-25

Harell G.S.; Guthaner D.F.; Breiman R.S.; Morehouse C.C.; Seppi E.J.; Marshall W.H.Jr; Wexler L., 1977: Cardiac computed tomography in vivo. Journal of Computer Assisted Tomography 1(3): 370

Monteleone, P.; Rocca, A. la; Fuschino, A.; Bortolotti, F.; Maj, M., 1999: Seasonal variation in plasma prolactin response to D-fenfluramine in healthy subjects. To assess dynamically a seasonal variation in the functioning of the central serotonin (5-HT) system, we investigated the prolactin (PRL) response to the specific serotonergic agent D-fenfluramine (D-FEN) in the different seasons of the year. Thir...