Supplementary Material for Bolstad chapter in Fundamentals of Data Mining in Genomics and Proteomics

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Introduction

The material on this page supplements the chapter entitled Pre-processing for DNA microarray data to be found in the book Fundamentals of Data Mining in Genomics and Proteomics. A greater description of the techniques used can be found there.

Pre-processing for Affymetrix GeneChips

The data used for this analysis was retrieved from the GEO, http://www.ncbi.nlm.nih.gov/geo/ stored as the data series GSE2603. This data was published in Minn et al (2005) Genes that mediate breast cancer metastasis to lung. Nature. 2005 Jul 28;436(7050):518-24. PubMed id: 16049480
LinkDescription
CodeR code for carrying out the analysis
Supplementary PlotsAdditional figures generated using the code

Pre-processing for two color microarrays

The data used for this analysis was retrieved from the GEO, http://www.ncbi.nlm.nih.gov/geo/ stored as the data series GSE1438. This data was published in Kuperman et al (2005) Dissecting asthma using focused transgenic modeling and functional genomics. J Allergy Clin Immunol. 2005 Aug;116(2):305-11. Pubmed id: 16083784
LinkDescription
CodeR code for carrying out the analysis
Supplementary PlotsAdditional figures generated using the code