R做差异表达分析问题
library(limma)
library(edgeR)
setwd(“G:Data treating/R/Difference analyse”)#将目标文件所在目录通过setwd命令设置为当前工作目录???
getwd()#查看目录是否设置成功
library(“readxl”)
rawdata1<-read_excel(“Practical theoretical difference.xlsx”,sheet = “Eukaryota”)
head(rawdata1)
rawdata<-as.matrix(t(rawdata1),colnames=NULL)#转置
write.table(rawdata, file = “Eukaryota.txt”,col.names = FALSE,row.names = TRUE, quote = F, sep="\t")
rawdata2<-read.delim(“Eukaryota.txt”,header = TRUE)
colnames(rawdata2)
y<-DGEList(counts=rawdata2[,2:477],genes=rawdata2[,1])
y<-DGEList(counts=y
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counts,genes=y
counts,genes=ygenes)
y_norm<-calcNormFactors(y)#默认为TMM标准化
#lcpm <- cpm(y)#每百万次计算计数(CPM)或每千字节读取(RPKM)
y<-plotMDS(y_norm,col=c(rep(“black”,238), rep(“red”,238)), dim = c(1, 2))#绘制二维散点图
group<-factor(c(rep(‘practical’,238),rep(‘theoretical’,238)))
design <- model.matrix(~group)
y<-DGEList(counts=rawdata2[,2:477],genes=rawdata2[,1])
dge <- estimateDisp(y, design = design, robust = TRUE) #估算离散值
结果出现错误:Error in solve.default(designunique, t(beta)) : no right-hand side in 'b’
真心不明白是什么意思。还希望各位指教一下。