Rscript for DEG

DEG_scripts/airway.group.txt

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+dex	SampleName	cell
+SRR1039508	untrt	GSM1275862	N61311
+SRR1039509	trt	GSM1275863	N61311
+SRR1039512	untrt	GSM1275866	N052611
+SRR1039513	trt	GSM1275867	N052611
+SRR1039516	untrt	GSM1275870	N080611
+SRR1039517	trt	GSM1275871	N080611
+SRR1039520	untrt	GSM1275874	N061011
+SRR1039521	trt	GSM1275875	N061011

DEG_scripts/create_testData.R

@@ -0,0 +1,34 @@
+suppressPackageStartupMessages(library(airway))
+suppressPackageStartupMessages(library(DESeq))
+suppressPackageStartupMessages(library(limma))
+suppressPackageStartupMessages(library(DESeq2))
+suppressPackageStartupMessages(library(edgeR)) 
+suppressPackageStartupMessages(library(pasilla))
+suppressPackageStartupMessages(library(pasilla))
+suppressPackageStartupMessages(library(Biobase))
+suppressPackageStartupMessages(library(CLL))
+data(sCLLex)
+data(pasillaGenes) 
+data(airway)
+
+write.table(exprs(sCLLex),file='sCLLex.expression.txt',quote = F,sep = '\t',row.names = T)
+exprSet=read.table('sCLLex.expression.txt',stringsAsFactors = F,header = T)
+write.table(pData(sCLLex)[,c(2,1)],file='sCLLex.group.txt',quote = F,sep = '\t',row.names = T)
+group=read.table('sCLLex.group.txt',stringsAsFactors = F,header = T)
+
+
+write.table(counts(pasillaGenes),file='pasillaGenes.expression.txt',quote = F,sep = '\t',row.names = T)
+exprSet=read.table('pasillaGenes.expression.txt',stringsAsFactors = F,header = T)
+write.table(pData(pasillaGenes)[,c(2,3)],file='pasillaGenes.group.txt',quote = F,sep = '\t',row.names = T)
+group=read.table('pasillaGenes.group.txt',stringsAsFactors = F,header = T)
+
+write.table(assays(airway)$counts,file='airway.expression.txt',quote = F,sep = '\t',row.names = T)
+exprSet=read.table('airway.expression.txt',stringsAsFactors = F,header = T)
+write.table(colData(airway) [,c(3,1,2)],file='airway.group.txt',quote = F,sep = '\t',row.names = T)
+group=read.table('airway.group.txt',stringsAsFactors = F,header = T)
+
+
+
+
+
+