midterm project

Course: Statistics in Bioinformatics

Date:20070430

指導教授 : 陳光琦學生 : 吳昱賢

What is BioConductor?

• What is BioConductor?

• As the website saying

• Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.

Outline

• 軟體資訊• 功能簡介• 相關教學• 使用心得

Bioconductor• R software project for the analysis and compreh

ension of biomedical and genomic data.– Gene expression arrays (cDNA, Affymetrix)– Pathway graphs– Genome sequence data

• Started in 2001 by Robert Gentleman, Dana Farber Cancer Institute.

• About 25 core developers, at various institutions in the US and Europe.

• Tools for integrating biological metadata from the web (annotation, literature) in the analysis of experimental metadata.

• End-user and developer packages.

Example R/BioC Packages

methods Class/method tools

tools

tkWidgets

Sweave(),gui tools

marrayTools, marrayPlots

Spotted cDNA array analysis

affy Affymetrix array analysis

annotate Link microarray data to metadata on the web

mva, cluster, clust, class

Clustering and classification

t.test, prop.test, wilcox.test

Statistical tests

wiki

• most of the content on this wiki is aimed at developers of Bioconductor packages.

Demo

• Install R and Bioconductor packages.

> MAplot(affybatch.example)

使用範例學習

R console

結論1.Bioconductor is a useful tool in dealing wit

h static problem on microarray

2.affy example show the power of the R

3. I benefit a lots from this report like how to use bioC in R.