transcriptome

transcriptome - The Goal Create a model of the...

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The Goal Create a model of the transcriptome using factor analysis Create model that simplifies and reveals structure in observed data by describing it as the result of hidden factors.
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Simple Example of Factor Analysis \ Observed Data – Grades for a class of students 4 problem set scores, 3 quiz scores, and 3 exam scores, 10 total variables Factor Models - There are many possible factor models to describe this dataset Factor Model A – 1 Factor, describing scholastic aptitude Factor Model B – 2 Factors, one describes problem sets, one describes exams+quizzes Factor Model C – 3 Factors, one each for problems sets, quizzes, and exams Factor Model D – 2 Factors, one for first half of course one one topic, one for second half of course on another topic Each model simplifies that data while maintaining much of the original information. The same thing can be done for gene expression data.
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The Gene Expression Data Gene Expression Omnibus Database Affymetrix U133A microarray platform 2,866 samples 22,215 transcripts per sample This is the data that is used to generate a factor model
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Data Preparation Download Data: 2.0 GB – approximately 65 million data points Parse data: Not exciting, but non-trivial Clean Data: Remove samples and transcripts that are missing data anywhere in the dataset. This only removes a small fraction of the data
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This note was uploaded on 11/11/2011 for the course BIO 7.344 taught by Professor Bobsauer during the Spring '08 term at MIT.

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transcriptome - The Goal Create a model of the...

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