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龙星课程—肿瘤生物信息学上机课程
曹莎
Email:[email protected]
How to get data from GEOquery
• source("http://bioconductor.org/biocLite.R")
biocLite("affy")
library(affy)
####download all the .CEL files
raw.data <- ReadAffy()
AffyRMA = rma(raw.data)
ExpRMA = exprs(AffyRMA)
write.table(ExpRMA, file="AffyRMA.txt")
A simple example about Batch effect removal
基因表达数据的双聚类分析
• Qubic 1.0
• http://csbl.bmb.uga.edu/~maqin/bicluster/faq
.html
• Documentation
• http://csbl.bmb.uga.edu/~maqin/bicluster/do
c/build/
• ./qubic -i data -f 0.25
各类数据的整合
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基因表达数据和metabolic profiling的数据
Pathview
Compound and gene data
Multiple states or samples
KEGG pathway

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