## Weighted analysis of paired microarray experiments

Venue: | Statistical Applications in Genetics and Molecular Biology |

Citations: | 5 - 3 self |

### BibTeX

@INPROCEEDINGS{Kristiansson_weightedanalysis,

author = {Erik Kristiansson and Anders Sjögren and Mats Rudemo and Olle Nerman and Erik Kristiansson and Anders Sjögren and Mats Rudemo and Olle Nerman},

title = {Weighted analysis of paired microarray experiments},

booktitle = {Statistical Applications in Genetics and Molecular Biology},

year = {},

pages = {2005}

}

### OpenURL

### Abstract

Copyright c○2005 by the authors. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the publisher, bepress, which has been given certain exclusive rights by the author. Statistical Applications in Genetics and Molecular Biology is produced by The

### Citations

2136 | Core Team. R: A Language and Environment for Statistical Computing - Development - 2008 |

547 | Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection - Li, Wong - 2001 |

500 | Normalization for cdna microarray data: a robust composite method addressing single and multiple slide systematic variation - Yang, Dudoit, et al. - 2002 |

387 | A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes
- Baldi, Long
- 2001
(Show Context)
Citation Context ...inverse gamma distribution is a conjugate prior distribution for the variance of a normal distribution and has as such been used in Bayesian and empirical Bayesian analysis of microarray data before (=-=Baldi and Long, 2001-=-; Lönnstedt and Speed, 2002; Smyth, 2004). The model can be summarised as follows: We observe Xg = (Xg1, . . . , XgNI ) where g = 1, . . . , NG. Let Σ be a covariance matrix with NI rows and columns, ... |

350 | Empirical bayes analysis of a microarray experiment - Efron, Tibshirani, et al. |

345 | Limma: linear models for microarray data
- Smyth
- 2005
(Show Context)
Citation Context ...ple standard deviations, according to Efron et al. (2001). Finally, the moderated t-statistic is included. It was developed and implemented by Smyth (2004) and it is available in the R package LIMMA (=-=Smyth et al., 2003-=-). The moderated t-statistic can be seen as a refined version of the B-statistic which was first presented in Lönnstedt and Speed (2002). In the paired microarray context, WAME is a generalisation of ... |

306 | Summaries of affymetrix GeneChip probe level data - Irizarry, Bolstad, et al. - 2003 |

301 | AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository - Edgar, Domrachev, et al. |

184 | models and empirical bayes methods for assessing differential expression in microarray experiments - Linear |

165 | Replicated microarray data - Lonnstedt, Speed - 2002 |

162 | The Bayesian Choice - Robert - 2001 |

98 | Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction. Bioinformatics - Wang - 2003 |

92 |
An Empirical Bayes approach to statistics
- Robbins
- 1955
(Show Context)
Citation Context ...tively few replicates, resulting in highly variable gene-specific variance estimates. To use the information in the large number of measured genes to handle this problem, an empirical Bayes approach (=-=Robbins, 1956-=-; Maritz, 1970) can be taken, determining a prior distribution from the data, thus moderating extreme estimates. This approach has been used in Baldi and Long (2001), Lönnstedt and Speed (2002) and Sm... |

39 |
N.: Continuous Univariate Distributions. Volume 2
- Johnson, Kotz, et al.
- 1995
(Show Context)
Citation Context ...nconditional distribution of Sg can be calculated by use of the fact that a gamma distribution divided by another gamma distribution has an analytically known distribution, a beta prime distribution (=-=Johnson et al., 1995-=-, page 248). Thus, which has the density function Sg | α ∼ 2 × β ′ ((NI − 1)/2, α) , (5) fSg | α(sg) = 1 Γ(α + (NI − 1)/2) (sg/2) 2 Γ(α)Γ((NI − 1)/2) (NI−1)/2−1 . α+(NI−1)/2 [1 + sg/2] http://www.bepr... |

33 |
BM: Low-level analysis of high-density oligonucleotide array data: background, normalization and summarization
- Bolstad
- 2004
(Show Context)
Citation Context ...is available, for example, shared sources of variation may be known. Quantitative quality measures may also be available, e.g. spot shape features or residuals from the fitting of probe-level models (=-=Bolstad, 2004-=-). It is possible to explicitly model some such sources of variation, for example using random or fixed effects (cf. Bakewell and Wit (2005)) and to include quality measures as covariates. However, su... |

23 |
Empirical Bayes Methods
- Maritz, Lwin
- 1989
(Show Context)
Citation Context ...icates, resulting in highly variable gene-specific variance estimates. To use the information in the large number of measured genes to handle this problem, an empirical Bayes approach (Robbins, 1956; =-=Maritz, 1970-=-) can be taken, determining a prior distribution from the data, thus moderating extreme estimates. This approach has been used in Baldi and Long (2001), Lönnstedt and Speed (2002) and Smyth (2004). 3 ... |

19 | A novel strategy for microarray quality control using Bayesian networks - Hautaniemi, Edgren, et al. - 2003 |

11 | Development of public toxicogenomics software for microarray data management and analysis - TONG, HARRIS, et al. - 2004 |

10 | Evaluation of quality-control criteria for microarray gene expression analysis - Dumur, Nasim, et al. - 2004 |

8 | Qa/qc as a pressing need for microarray analysis: meeting report from camda’02 - Johnson, Lin |

6 | E (2005) Weighted analysis of microarray gene expression using maximum-likelihood - DJ, Wit |

6 |
Application and optimization of microarray technologies for human postmortem brain studies
- Ryan, Huffaker, et al.
- 2004
(Show Context)
Citation Context ...i et al. (2004). Despite the observed need for effective quality control, standard operating procedures for quality assurance of the entire chain of processing steps have only recently been proposed (=-=Ryan et al., 2004-=-, for one-channel experiments). However, even utilising an optimal quality control procedure aiming at removing low quality arrays and/or individual gene measurements (e.g. spots), there will always b... |

4 | Diagnostic plots for detecting outlying slides in a cDNA microarray experiment - Park - 2005 |

4 | WE Jr: Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain. Biol Psychiatry 2004 - Tomita, MP, et al. |

3 | DT: A graphical approach for quality control of oligonucleotide array data - Chen |

2 |
Bioconductor R packages for exploratory data analysis and normalization of cDNA microarray data
- Dudoit, Yang
- 2003
(Show Context)
Citation Context ...v) the moderated t-statistic of Smyth (2004). Next, WAME is applied to three real datasets, the Cardiac dataset of Hall et al. (2004), the Polyp dataset of Benson et al. (2004) and the Swirl dataset (=-=Dudoit and Yang, 2003-=-). The results obtained are discussed in a subsequent section and some derivations and mathematical details are given in an appendix. 2 Background To put the quality control aspect of our model into c... |