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## Analysis of variance for gene expression microarray data (2000)

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### Other Repositories/Bibliography

Venue: | Journal of Computational Biology |

Citations: | 362 - 5 self |

### Citations

2895 | Cluster analysis and display of genome-wide expression patterns” - Eisen, Spellman, et al. - 1998 |

2461 | Generalized additive models
- Hastie, Tibshirani
- 1990
(Show Context)
Citation Context ...onstant error variance 2 . To further examine the distribution of residuals, we plotted the absolute value of each residual against the � tted values log.yij \ kg/ and � t a local regression curve (=-=Hastie and Tibshirani, 1990-=-, p. 29). Fig. 3a shows there is no overwhelming trend in the absolute size of the residuals, with only a very slight trend towards larger residuals for the smallest and largest � tted values. The fac... |

1550 |
Applied Regression Analysis,
- Draper, Smith
- 1981
(Show Context)
Citation Context ...d allows more degrees of freedom for estimating error variance. It is common practice in applied statistics to seek a transformation of the raw data to obtain normal residuals with constant variance (=-=Draper and Smith, 1998-=-). In this study we have applied a logarithm transformation to the � uorescent intensities. The residual distribution on the log scale is nonnormal, but we did not detect any dramatic evidence against... |

802 | Randomization, Bootstrap and Monte Carlo Methods - Manly - 1997 |

769 |
Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation”
- Tamayo, Slonim, et al.
- 1999
(Show Context)
Citation Context ...rom the experiment (Fisher, 1935, p. 60). Looking ahead, we believe they will also be useful in assessing the quality of the results from higher-order analyses such as clustering (Eisen et al., 1999; =-=Tamayo et al., 1999-=-). In this work, we perform analysis of variance on microarray data from two designed experiments that used independent arrays to study the same tissue samples. We employ a bootstrapping technique to ... |

705 | The design of experiments. - Fisher - 1935 |

575 |
Bootstrap method for standard error, confidence intervals, and other measures of statistical accuracy. Statistical Science
- Efron, Tibshirani
- 1986
(Show Context)
Citation Context ...ed, as illustrated in Fig. 2a. These observations suggest that the usual con� dence intervals based on normal theory are not appropriate. Therefore, we employed a bootstrap analysis of the residuals (=-=Efron and Tibshirani, 1986-=-) to address this question.s824 KERR ET AL. Using the bootstrap, we produced a set of simulated datasets log.yij kg/ ¤ , where log.yij kg/ ¤ D O C OAi C ODj C OVk C OGg C .cAG/ig C . cVG/kg C ¤ ij ... |

443 |
Experimental designs.
- Cochran, Cox
- 1957
(Show Context)
Citation Context ...to the design factors, array and Table 1. The Latin Square Design Array Dye 1 2 Red Liver Muscle Green Muscle Livers822 KERR ET AL. dye, the layout of the tissue varieties forms a 2 £ 2 Latin square (=-=Cochran and Cox, 1992-=-). We therefore refer to this as the Latin square design (it is sometimes called a “dye-swap” experiment). Given the factors in our model, there are sixteen possible effects when we consider interacti... |

428 |
Exploring the new world of the genome with DNA microarrays.
- BROWN, BOTSTEIN
- 1999
(Show Context)
Citation Context ...pression pro� les of many genes can provide additional insights into physiological processes or disease etiology that is mediated by the coordinated action of sets of genes. Spotted cDNA microarrays (=-=Brown and Botstein, 1999-=-) are emerging as a powerful and cost-effective tool for large scale analysis of gene expression. In the � rst step of the technique, DNA clones with known sequence content are spotted and immobilized... |

366 | Ratio-Based Decisions and the Quantitative Analysis of cDNA
- Chen, Dougherty, et al.
- 1997
(Show Context)
Citation Context ...rectly normalizes microarray data and yields reproducible estimates. DISCUSSION A common practice with microarray data is to compute ratios of the raw signals as estimates of differential expression (=-=Chen et al., 1997-=-). We � nd this approach to be inadequate for several reasons. It is natural and convenient to speak of fold change in expression, but it can also be misleading becauses832 KERR ET AL. ratios expressi... |

265 | On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data.
- Newton, Kendziorski, et al.
- 2001
(Show Context)
Citation Context ...be too extreme. This can be addressed by treating the gene and variety£gene terms as random effects in the ANOVA model (Robinson, 1991). This approach leads to “shrinkage” estimators for these terms (=-=Newton et al., 2000-=-). We view these problems as areas that are ripe for further investigation in the context of the analysis of well-designed microarray experiments. Tissue acquisition METHODS Human liver and skeletal m... |

199 |
That BLUP is a good thing: the estimation of random effects.
- ROBINSON
- 1991
(Show Context)
Citation Context ...e being estimated, the estimates of the highest and lowest effects will tend to be too extreme. This can be addressed by treating the gene and variety£gene terms as random effects in the ANOVA model (=-=Robinson, 1991-=-). This approach leads to “shrinkage” estimators for these terms (Newton et al., 2000). We view these problems as areas that are ripe for further investigation in the context of the analysis of well-d... |

29 |
Optimal incomplete block designs.
- John, Mitchell
- 1977
(Show Context)
Citation Context ...sible for microarrays because only one sample can correspond to each array–dye combination. However it is possible to derive ef� cient designs that satisfy the constraints imposed by this technology (=-=John and Mitchell, 1977-=-; Cheng, 1978). In general, for a given number of arrays, designs that are balanced across the samples of interest will provide the greatest ef� ciency. In our studies, using two arrays each, we prefe... |

17 |
Optimality of certain asymmetrical experimental designs.
- Cheng
- 1978
(Show Context)
Citation Context ...ause only one sample can correspond to each array–dye combination. However it is possible to derive ef� cient designs that satisfy the constraints imposed by this technology (John and Mitchell, 1977; =-=Cheng, 1978-=-). In general, for a given number of arrays, designs that are balanced across the samples of interest will provide the greatest ef� ciency. In our studies, using two arrays each, we prefer the Latin s... |

6 | The approximate randomization test as an alternative to the F test in analysis of variance - Still, White - 1981 |

4 | Expression pro� ling using cDNA microarrays. Nature Genetics Supplement - Duggan, Bittner, et al. - 1999 |

3 |
Estimating the posterior probability of gene expression from microarray data
- Sapir, Churchill
- 2000
(Show Context)
Citation Context ...tios (Eisen, 1999). Further, exploration of untransformed data and the examination of other transformations (square-root, reciprocal, etc.) led us to conclude that the log transform is a good choice (=-=Sapir and Churchill, 2000-=-). The terms A, D, and V in the ANOVA model are used to capture differences that occur between different arrays, dyes, and varieties. However, these terms also capture all of the higher-order interact... |