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hms_8915

# hms_8915 - Harvard-MIT Division of Health Sciences and...

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Mar 18, 2004 Genomic Medicine HT 512 Data representation, transformation & modeling in genomics Lecture 11, Mar 18, 2004 Alvin T. Kho Children's Hospital Boston Dana-Farber Cancer Institute Harvard-MIT Division of Health Sciences and Technology HST.512: Genomic Medicine Prof. Alvin T.Kho

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Mar 18, 2004 Lecture Outline 2 prototypical study design Background concepts 2-way comparison “Noise” Time series “Replicates”, reproducibility Data representation (DR) Normalization What is DR ? “Fold” Measurement device to Miscellany spreadsheet Dimensionality - scales Transformations / Changes-of-coordinates
Mar 18, 2004 Prototype study 1: 2-way comparison Molecular differences in adipocytes of type-2 Diabetes vs Normal humans. 27 type-2 diabetes patients. 11 normal patients. arrays. Pre-study reality check: Stratification – clinical phenotype. Partial math formulation: Let D = chip data of j-th Diabetic. N j = j-th j Normal. D , N j are vectors/matrices whose dimensions depend j upon # genes/parameters/variables measured per sample. Next steps ...

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Mar 18, 2004 Prototype study 2: Time series RNA expression profile of a developing whole mouse pancreas at time points P1 to P60. Pre-study reality check: Stratification – histology, regulation. Partial math formulation: Let T = chip data of j-th developmental j stage are vectors/matrices whose dimensions depend upon # genes/parameters measured per sample. Next steps ... patterns
Mar 18, 2004 What is DR? A mathematical re formulation of a scientific, real-world problem. Mapping observations and measurements to a set of symbols (typically, real numbers) that can be acted upon by an algebra. The form of representing the data values in the integrated dataset, including any numerical type conversion or re- classification that was performed. Usually this will involve only type conversions, although occasionally actual numerical changes may have been necessary. The units and precision are also indicated. [ www.ngdc.noaa.gov ] Something to do with database annotation and standards. Multimedia: Charts, graphs, plots.

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Mar 18, 2004 Device to Spreadsheet: Know measuring device Understand general principles of measurement Relevance of scanner / device settings Phosphor imager mechanism 1-/2-channel (competitive hybridization) ?
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