GSE1009

  1. library(AnnoProbe)
  2. suppressPackageStartupMessages(library(GEOquery))
  4. ## 使用AnnoProbe 获取数据
  5. gset=AnnoProbe::geoChina('GSE1009')
  7. # check the ExpressionSet
  8. eSet=gset[[1]]
  9. # extract the expression matrix and phenotype data
  10. probes_expr <- exprs(eSet);dim(probes_expr)
  11. head(probes_expr[,1:4])
  12. boxplot(probes_expr,las=2)
  13. probes_expr=limma::normalizeBetweenArrays(probes_expr)
  14. boxplot(probes_expr,las=2)
  15. ## pheno info
  16. phenoDat <- pData(eSet)
  17. head(phenoDat[,1:4])
  19. ## check GPL and annotate the probes to genes.
  20. gpl=eSet@annotation
  21. checkGPL(gpl)
  22. printGPLInfo(gpl)
  23. probe2gene=idmap(gpl)
  24. head(probe2gene)
  25. genes_expr <- filterEM(probes_expr,probe2gene )
  26. head(genes_expr)
  28. # do DEG
  29. ## define the group
  30. group_list= c(rep('Control',3),rep('Diabetes',3))
  31. table(group_list)
  33. ## Create DEGContainer
  34. data_i <- Create_DEGContainer(
  35.   species = "Human",
  36.   dataType = "Array",
  37.   expMatrix = genes_expr,
  38.   groupInfo = group_list,
  39.   caseGroup = "Diabetes",idType = "SYMBOL",filterMethod = NULL
  40. )
  42. ## Run workflow
  43. data_o <- runALL(data_i,dir = "testArray",top = 10,parallel = T,GO = T,KEGG = T)