lecture-25-handouts - 11/15/2011 Practical Bioinformatics...

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1 Practical Bioinformatics for Life Scientists Week 13, Lecture 25 István Albert Bioinformatics Consulting Center Penn State R for high throughput data analysis Strengths extensive statistical libraries data frames outstanding data structure “loop - less” transformations and indexing it just works on every platform with (minimal installation woes) Weaknesses the environment seems to have some design ambiguities ( or perhaps I don’t understand it well enough - though I tried ) often it is difficult to identify what an object actually is/does silent errors and default behaviors Personal observations on complex bioinformatics R packages Often built by novice programmers Usually overspecialized work for only one type of problem and with tacit assumptions Riddled with extremely subtle errors and unexpected behaviors (bug or feature?) Many were designed to be a black box Exceedingly difficult to trace the chain of events and/or verify that a result is correct! R and BioConductor
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This note was uploaded on 02/29/2012 for the course BMMB 597D taught by Professor Istvanalbert during the Fall '11 term at Pennsylvania State University, University Park.

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lecture-25-handouts - 11/15/2011 Practical Bioinformatics...

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