GEO数据下载
library(GEOquery)
eSet = getGEO("GSE162550",destdir = F,getGPL = F)#按芯片方式下载
rm(list = ls())
dat=
read.table("GSE162550_gene_sample_count_with_symbol.xls",
fill = T,sep = "\t",header = T)
table(!duplicated(dat$Symbol))
o = order(rowSums(dat[,4:9]),decreasing = T)
dat = dat[o,]
dat = dat[!duplicated(dat$Symbol),]
dat = dat[dat$Symbol!="---",]
exp = dat[,4:9]
rownames(exp) = dat$Symbol
exp=exp[apply(exp,1,function(x){sum(x>0)>4}),]
Group=rep(c("DMSO","DHA"),each=3)
Group=factor(Group,levels=c("DMSO","DHA"))
proj="DHA"
save(exp,Group,proj,file=paste0(proj,"_gdc.Rdata"))
#接下来可以进行下一步，差异基因的分析
讲文献1：
image.png
先做的hub基因，是为了在火山图上标注出来
文献2：
文献3
image.png
