y 基礎分
析
在家也能作的分析
董建億
System requirement
Hardware :
CPU: at least P4
4Gb RAM in 64-bite OS is strongly recommended! But, with great patience, 2 Gb in 32-bit OS is OK.
Software:
R GUI environment
http://cran.csie.ntu.edu.tw/ MultiExperimentViewer
http://sourceforge.net/projects/mev-tm4/files/latest/download LucasLazyPack.Zip
http://lucas.genome-analyst.org/tools/lucaslazypack
Software Installation
• Download MeV and Unzip in your Hard Drive (ex. D:\ )
• Download LucasLazyPack.zip and unzip into R folder of MeV (D:\MeV_x_x_x\R-x.x.x)
• Run RunMeFirst.bat/.sh
Visit the web site for related materials:
http://lucas.genome-analyst.org/activities-articles/course/nrpb2011q4
1
General Analysis workflow
Data preprocessing
Normalization
Signal adjustment (flag, flooring…) Probe summarization
Signal transform (fold change, log transform)
Data QC/QA
QC index (Hybridization control) Visualization (PCA, MDS, Box plot..)
Find differentially expressed genes
Statistical analysis p-Value correction
Biological interpretation
Gene annotation Gene set analysis Gene network analysis
Data preprocessing and QC/QA
Normalization
Load CEL files
Select normalization algorithms Show QC report
Save result
Signal Flooring
Load data file (Signal matrix) Select flooring level
Save result
Multidimensional scaling
Load Data matrix Assign data point Show MDS plot
