Index

Affy package, 83Affymetrix, 3–7, 26, 28, 29AIDA Array Metrix, 19AMADA, 43Amino-allyl-dUTP, 6Anchoring enzyme, 11ANOVA, 30, 38, 81Archaea, 73ArrayExpress, 79ArrayFox, 19ArrayPro, 20ArrayVision, 20AvgDiff, 26, 28

Background correction, 17Bead arrays, 9Benjamini and Hochberg, 31Bioconductor, 34, 80, 83, 85Biotin, 5BLAST, 74Bonferroni correction, 30, 32

Cantilever, 12cDNA arrays, 6Censoring, 66Classification, 54, 56CLIFF, 53Clustering, 44Codon usage, 74Correspondence analysis, 37, 43, 82Cox Proportional Hazards, 67, 85

Cancer Diagnostics with DNA Microarrays, By Steen KnudsenCopyright c© 2006 John Wiley & Sons, Inc.

cRNA, 5Cross-hybridization, 74Cy3, 6Cy5, 6CyberT, 30

Dapple, 19Dchip, 35Digital Micromirror Arrays, 8Distance measures, 47DNAprocessor, 8Dye bias, 25

Effect sizes, 70Escherichia coli, 73Euclidean distance, 47, 49Eukaryote, 73European Bioinformatics Institute, 80Excel, 78Expression analysis, 3Expression index calculation, 26Expression profile, 3Expression Profiler, 80

F-Scan, 19False Discovery Rate, 31FDR, 31Febit, 8File format, 79Fisher’s inverse chi-square method, 70Fixed-effects model, 70

183

184 INDEX

Fold change, 28Fragmentation, 5

Gene Expression Omnibus, 79Gene finding, 73Gene normalization, 51Gene shaving, 43, 53GeneCluster, 80GenePix Pro, 20Geniom, 8Genotyping, 3Ghost, 18Gridding, 16GridGrinder, 19GST-PRIME, 76

Hidden Markov models, 74Hierarchical clustering, 45, 46Hybridization, 1

ICA, 39IconoClust, 20Image analysis, 16ImaGene, 20Independent component analysis, 39Inkjet arrays, 8

J-Express, 42

K nearest neighbor classifier, 56, 83K-means clustering, 46Kaplan–Meier, 66, 85Koadarray, 20

Leave-one-out cross validation, 56Log-rank test, 66Logit-t, 27Long oligonucleotide probes, 75LOOCV, 56Lowess, 24Lucidea, 20

MAGE-ML, 79Mann-Whitney, 30Matrix, 26, 37, 39, 41, 44, 49, 52, 82Matthews correlation, 58MBEI, 26Meta-analysis, 69MGED, 79MIAME, 79Microarray Suite, 20MicroVigene, 20Mismatch, 5, 26Mixed cell populations, 33MM, 5, 26Multiple testing, 30Mutation, 5

MVA plot, 22, 23

Nearest Centroid classifier, 57Neural network, 57, 83NimbleGen, 8Nonparametric tests, 30Nonspecific hybridization, 5, 26Normality, 30Normalization, 22, 51Northern blotting, 1

OligoArray, 76, 173Oligonucleotide, 1OligoWiz, 75Open reading frame, 73Outlier detection, 28Overfitting, 56

P-Scan, 19P -value, 30Partial Least Squares, 39PCA, 37, 39, 41, 82PCR, 74PDNN, 27Pearson correlation coefficient, 48Pearson distance, 49Perfect match, 5, 26Performance evaluation, 58Phoretics array, 20Photolithography, 4PLS, 39PM, 5, 26Polylysine, 6Position dependent nearest neighbor model, 27Principal component analysis, 37Print tip bias, 25Probe, 2, 3Probe remapping, 76Probe-to-gene mapping, 76Probes, 75ProbeWiz, 74Prokaryote, 73Promoters, 74PSI-BLAST, 77

Qspline, 24Quantarray, 20Quantile normalization, 24

R, 80, 83R programming language, 85Random-effects model, 70Rank sum, 30Remapping of probes, 76Replicate, 80Reverse transcriptase, 5RMA, 27

INDEX 185

RNeasy, 5Robot, 3Robust Multiarray Average, 27

S-PLUS, 85SAGE, 3, 10SAM, 32SAS, 85ScanAlyze, 19Segmentation, 17Self-organizing maps, 46Sensitivity, 58Serial analysis of gene expression, 3,

10Signal (MAS 5.0), 26Significance, 29Small, round blue cell tumors, 59Southern blotting, 1Spatial bias, 18, 25Spike controls, 25Splice sites, 74Spot, 20Spotfinder, 19Spotted arrays, 6SPSS, 85Standard deviation, 52

Standardization, 79Stanford Microarray Database, 79Statistical analysis, 80Streptavidin-phycoerythrin, 5Succinic anhydride, 6Supervised PCA, 39Support vector machine, 58Surgery, 54Survival analysis, 66, 85SVDMAN, 42

t-Test, 29–31, 38, 81T7 RNA polymerase, 5Time-series, 51Tree harvesting, 64TRIzol, 5

UCSF Spot, 19

Validation, 56Vector

angle, 48, 52angle distance, 49

Wilcoxon, 30, 81