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Biochip Platform- BioConductor 陳彥如 許家維 許文馨 游崇善. 2 BioConductor 優缺點...
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Transcript of Biochip Platform- BioConductor 陳彥如 許家維 許文馨 游崇善. 2 BioConductor 優缺點...
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/