Journal of Animal and Veterinary Advances

Year: 2012
Volume: 11
Issue: 24
Page No. 4593 - 4598

Comparison of Effect of Non-Specific Filtering Methods and their Combinations on GeneChip Data Analysis: A Case for Affymetrix Porcine Genome Microarray

Authors : Ming Zhao, Hong-Bo Chen, Xiang-Dong Liu, Chao Wang, Jing-Ying Guo, Min-Hui He, Shu-Hong Zhao and Meng-Jin Zhu

References

Archer, K.J. and S.E. Reese, 2010. Detection call algorithms for high-throughput gene expression microarray data. Brief Bioinfo., 11: 244-252.
CrossRef  |  PubMed  |  Direct Link  |  

Auer, H., D.L. Newsom and K. Kornacker, 2009. Expression profiling using affymetrix genechip microarrays. Methods Mol. Biol., 509: 35-46.
CrossRef  |  PubMed  |  Direct Link  |  

Bourgon, R., R. Gentleman and W. Huber, 2010. Independent filtering increases detection power for high-throughput experiments. Proc. Natl. Acad. Sci. USA., 107: 9546-9551.
CrossRef  |  PubMed  |  Direct Link  |  

Calza, S., W. Raffelsberger, A. Ploner, J. Sahel and T. Leveillard et al., 2007. Filtering genes to improve sensitivity in oligonucleotide microarray data analysis. Nucleic. Acids. Res., Vol. 35. 10.1093/nar/gkm537

Chen, H., C. Li, M. Fang, M. Zhu and X. Li et al., 2009. Understanding Haemophilus parasuis infection in porcine spleen through a transcriptomics approach. BMC Gen., Vol. 10. 10.1186/1471-2164-10-64

Gentleman, R.C., V.J. Carey, D.M. Bates, B. Bolstad and M. Dettling et al., 2004. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol., Vol. 5. 10.1186/gb-2004-5-10-r80

Gohlmann, H. and W. Talloen, 2009. Gene Expression Studies Using Affymetrix Microarrays. Chapman, Hall, London,ISBN-13: 978-1420065152, Pages: 359..

Hackstadt, A.J. and A.M. Hess, 2009. Filtering for increased power for microarray data analysis. BMC Bioinfo., Vol. 10. 10.1186/1471-2105-10-11

Hubbell, E., W.M. Liu and R. Mei, 2002. Robust estimators for expression analysis. Bioinformatics, 18: 1585-1592.
CrossRef  |  Direct Link  |  

Jiang, Z. and R. Gentleman, 2007. Extensions to gene set enrichment. Bioinformatics, 23: 306-313.
CrossRef  |  Direct Link  |  

Kauffmann, A. and W. Huber, 2010. Microarray data quality control improves the detection of differentially expressed genes. Genomics, 95: 138-145.
CrossRef  |  PubMed  |  Direct Link  |  

Lusa, L., E.L. Korn and L.M. McShane, 2008. A class comparison method with filtering-enhanced variable selection for high-dimensional data sets. Stat Med., 27: 5834-5849.
CrossRef  |  PubMed  |  Direct Link  |  

McClintick, J.N. and H.J. Edenberg, 2006. Effects of filtering by Present call on analysis of microarray experiments. BMC Bioinf., Vol. 7. 10.1186/1471-2105-7-49

Mieczkowski, J., M.E. Tyburczy, M. Dabrowski and P. Pokarowski, 2010. Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements. BMC Bioinfo., Vol. 11. 10.1186/1471-2105-11-104

Okoniewski, M.J., Y. Hey, S.D. Pepper and C.J. Miller, 2007. High correspondence between Affymetrix exon and standard expression arrays. Biotechniques, 42: 181-185.
PubMed  |  Direct Link  |  

Prieto, C., A. Risueno, C. Fontanillo and J. de las Rivas, 2008. Human gene coexpression landscape: Confident network derived from tissue transcriptomic profiles. PLoS One, Vol. 3. 10.1371/journal

Talloen, W., D.A. Clevert, S. Hochreiter, D. Amaratunga, L. Bijnens, S. Kass and H.W. Gohlmann, 2007. I/NI-calls for the exclusion of non-informative genes: A highly effective filtering tool for microarray data. Bioinformatics, 23: 2897-2902.
CrossRef  |  PubMed  |  Direct Link  |  

Wu, Z. and R.A. Irizarry, 2004. Preprocessing of oligonucleotide array data. Natr. Biotechnology, 22: 656-658.
PubMed  |  Direct Link  |  

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