Biochip Platform-BioConductor

陳彥如 許家維許文馨 游崇善

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BioConductor 優缺點

優點 免費軟體 圖形介面 根據使用者需求修改程式

缺點 需詳知函式名稱 必需清楚知道程式邏輯

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Installation of Bioconductor

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Bioconductor Packages

Bioconductor Task View: BiocViews Subviews

Software AnnotationData ExperimentData

Packages in view No packages in this view

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Bioconductor Packages - Software

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marrayPlots: boxplots of log-ratios log_2 R/G by print-tip group, maBoxplot function

affy: image of Affymetrix probe-level intensities, image function

affy: MA-plots for three chips, mva.pairs function

edd: stratified matrix boxplots, matbox.strat function

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geneplotter: Comparing mean expression levels between two groups

hexbin: Plot distinguishing cells between two hexbin objects, hdiffplot function

marrayPlots: image of Cy3 background intensities, maImage function

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Bioconductor Packages - Others

AnnotationData It provide annotation on the genes on microarra

ys This resource can be searched by organism, ch

ip manufacturer, chip name etc.ExperimentData

They contain published data pre-prepared for Bioconductor

Many of the tutorials (vignettes) in Bioconductor use these data in exercises.

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Vignettes

Each Bioconductor package contains at least one vignette

提供以任務為目的來描述物件功能Vignettes contain executable examples an

d are intended to be used interactively.

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Classes and Methods

the Bioconductor packages have adopted the class/method object-oriented programming (OOP) paradigm Classes are objects that follow a particular form

at Methods are functions, such as plot, that behav

e differently depending on class

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資料來源

台大生物資訊學導論 http://homepage.ntu.edu.tw/~lyliu/IntroBioinfo/

Bioconductor http://www.bioconductor.org/