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龙星课程 — 肿瘤 生物 信息学上机课程

龙星课程 — 肿瘤 生物 信息学上机课程. 曹莎 Email:scaorobin@sina.com. How to get data from GEOquery. source("http://bioconductor.org/ biocLite.R ") biocLite (" affy ") library( affy )

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龙星课程 — 肿瘤 生物 信息学上机课程

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  1. 龙星课程—肿瘤生物信息学上机课程 曹莎 Email:scaorobin@sina.com

  2. How to get data from GEOquery • source("http://bioconductor.org/biocLite.R") biocLite("affy") library(affy) ####download all the .CEL filesraw.data <- ReadAffy()AffyRMA = rma(raw.data)ExpRMA = exprs(AffyRMA)write.table(ExpRMA, file="AffyRMA.txt")

  3. A simple example about Batch effect removal

  4. 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/doc/build/ • ./qubic -idata -f 0.25

  5. 各类数据的整合 • 基因表达数据和metabolic profiling的数据 • Pathview • Compound and gene data • Multiple states or samples

  6. KEGG pathway

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