Transcript midterm project

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
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軟體資訊
功能簡介
相關教學
使用心得
Bioconductor
• R software project for the analysis and
comprehension 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
marrayTools,
marrayPlots
Sweave(),gui tools
affy
Affymetrix array analysis
annotate
Link microarray data to metadata
on the web
Clustering and classification
Spotted cDNA array analysis
mva, cluster,
clust, class
t.test, prop.test, Statistical tests
wilcox.test
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
with 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.