04%20preNormalization%20cDNA%201_22_08

04%20preNormalization%20cDNA%201_22_08 - 1 1...

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Unformatted text preview: 1 1 Pre-normalization Methods for Two-Color Microarray Data 1/22/2008 2 Pre-normalization analysis Image processing Background correction Filtration Transformation 3 From this image 4 We get a data table that usually includes Header: information about scanning software information, filenames, measurement parameters and quality settings, etc. Raw data: the location, geneID, intensity measurements and quality measurements, 5 We get the data table (truncated) Header Begin Raw Data Field Meta Row Meta ColuRow Column Gene ID Flag Signal MedianSBackground Median A 1 1 1 1 MZ00040724 1645.5 533 A 1 1 1 2 MZ00040730 2 613 469 A 1 1 1 3 MZ00040748 741.5 462 A 1 1 1 4 MZ00040754 909 473 A 1 1 1 5 MZ00040772 964 471.5 A 1 1 1 6 MZ00040778 2 574 469 A 1 1 1 7 MZ00040796 2 579 487 A 1 1 1 8 MZ00040802 3 38051 614 A 1 1 1 9 MZ00013020 3 4539 516.5 A 1 1 1 10 MZ00013026 3 597.5 491.5 A 1 1 1 11 MZ00013044 3 16210 521.5 Show the partial raw data in excel file. 6 Which intensity measurement to use? There is no clear conclusion to use a particular intensity measurement over the others. Popular values to use: median/trimmed mean (robust) and mean (good for data without outliers). We will use median intensity values of each spot: Signal Median ( SMD ) Background Median ( BMD ) 2 7 After retrieving image data Background correction Filtration Transformation The order of the three steps is not fixed, the purpose is to process the data to be easier/better to analyze. 8 Assumption: the measured signal intensity (S, foreground) is a summation of fluorescence of labeled target sample (T) and fluorescence of background (B) S = B + T ....
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This note was uploaded on 08/26/2009 for the course STAT 416 taught by Professor Peng,l during the Spring '08 term at Iowa State.

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04%20preNormalization%20cDNA%201_22_08 - 1 1...

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