Analyzing Microarray Gene Expression Data .ppt

It is assumed that the logged expression levels have been preprocessed with adjustment for array effects. Majority of time on a data analysis project will be spent “cleaning” the data before doing any analysis Paradoxically, most statistical training assumes that the data arrive “prelceaned.” Students, whether in PhD programs or an undergraduate introductory course, are not taught routinely to check data for accuracy or even to worry about it. Exacerbating the problem further are claims by software vendors that their techniques can produce valid results no matter what the quality of the incoming data. De Veaux and Hand How to Lie with Bad Data, Statist. Sci., 2005 Contents Distribution of References by Year It is assumed that the logged expression levels have been preprocessed with adjustment for array effects. mRNA is extracted from the cell Microarrays Indirectly Measure Levels of mRNA mRNA is reverse transcribed to cDNA mRNA itself is unstable The sample is hybridized to known DNA sequences on the array tens of thousands of genes PROBE cDNA is labeled with fluorescent dye TARGET If present, complementary target binds to probe DNA complementary base pairing Target bound to probe DNA fluoresces mRNA from the cell sample is washed over the surface – HYBRIDIZATION The microarray experiment measure the amount of bound mRNA at each spot Allows the measurement of expression for thousands of genes from the amount of bound mRNA. A Spotted cDNA Microarray Experiment Compare the gene expression levels for two cell populations on a single microarray. e.g. tumour and normal cells Microarray Image Red: High expression in target labelled with cyanine 5 dye Green : High expression in target labelled with cyanine 3 dye Yellow : Similar expression in both target samples Assumptions: Gene Expression mRNA Fluorescence Intensity 1 2 cellular mRNA levels directly reflect gene expression intensity of bound target is a measure of the abundance