Study of gene expression of human liver Hepatocellular carcinoma

Expression profiling by array
We have profiles 268 HCC tumor, 243 adjacent non-tumor, 40 cirrhotic and 6 healthy liver samples.

2020年12月22日09:00:20

问题一

没有现成的包,读取gpl页面的soft文件，按列取子集,读取速度太慢，直接去GEO官网下载SOFT文件再用下面代码

  1. # 
  2. library(GEOquery)
  3. kl2 = read.table(file = )
  4. kl2 = getGEO(gpl,destdir = ".")
  5. kl1=kl2@dataTable@table
  6. ids = kl1[,c(1:3)]
  7. colnames(ids)
  8. colnames(ids) = c("probe_id","ENTREZID","SYMBOL") #改名方便后面使用
  9. head(ids)

GSE25097 - 图1

问题二 图片保存大小

  1. ggsave(p2,filename = paste0(gse,"3in1.png"),limitsize = FALSE,
  2. +        width = 16, height = 9)