1. Project of CZ5225 case study by using SOFT format from GEO
Zhang Jingxian:

2. Installation R & Bionconductor
Install R from:
Open R platform then execute:
>source("
>biocLite()
>biocLite(“GEOquery”)
Check library by execute: >library()

3. Case study of using SOFT format for dataset without raw data
Dataset source (GSE19697):

4. Create title.txt (the third column is useless but can fix a
bug in later):
Each column is
Separated by
“\t”

5. Set workdir by execute: Load modules by execute:
Open R
Set workdir by execute:
>setwd(‘d://gse19697’)
Load modules by execute:
>library(simpleaffy)
>library(GEOquery)
Load data by:
>g <- getGEO(‘GSE19697')

6. Make expression set eset by:
>p <- read.table("title.txt",row.name=1,header=TRUE,sep="\t")
>pd <- new ("AnnotatedDataFrame",data=p)
eset <- new("ExpressionSet", exprs = exprs(g),phenoData = pd)
Compare two groups by:
>pc.result <- pairwise.comparison(eset.rma, "title", c("pCR", “RD"), logged=FALSE, method="logged")

7. Filter significant change markers between two goups by:
>significant <- pairwise.filter(pc.result,fc=log2(1.5), tt=0.001)

8. Plot significant changed markers: Annotate selected markers:

10. Annotate selected markers:

11. Useful resources http://www.bioconductor.org/