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  1. # your code goes here
  2. library(GEOquery)
  3. library("ALL")
  4. gse <- getGEO("GSE189086", GSEMatrix=TRUE,AnnotGPL = TRUE)
  5. length(gse)
  6. gse<-gse[[1]]
  7. Data<-exprs(gse)
  8. str(Data)
  9. gse
  10. Data.class<-class(Data)
  11. Data.class
  12. attributes(Data)
  13. Data.dim<-dim(Data)
  14. Data.dim
  15. Data<-Data[1:20,]
  16. attributes(Data)
  17. dim(Data)
  18. str(Data)
  19. heatmap(Data)
  20. mock<-Data[,c(1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31)]
  21. infected<-Data[,c(2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32)]
  22. #t-test
  23. infected.summary <- summary(infected)
  24. infected.summary
  25. mock.summary <- summary(mock)
  26. mock.summary
  27. mock.mean<-apply(mock,1,mean,na.rm=TRUE)
  28. infected.mean<-apply(infected, 1,mean,na.rm=TRUE)
  29. Data.test<-t.test(x=mock,y=infected,var.equal=TRUE)
  30. Data.test
  31. #boxplot_for_control_test
  32. boxplot(mock, notch=F,varwidth=T,main="Mock boxplot", outline=TRUE,las=2,col="#8EEC9C")
  33. boxplot(infected, notch=F,varwidth=T,main="Infected boxplot", outline=TRUE,las=2,col="#F08080")
  34. m<-rep("1",16)
  35. i<-rep("0",16)
  36. GeneSamples<-paste(m,i,sep = "",collapse = "")
  37. sml<-strsplit(GeneSamples,split = "")[[1]]#notice
  38. gs<-factor(sml)
  39. ord <- order(gs)
  40. groups <- make.names(c("mock","infected"))
  41. palette(c("#B580F5", "#33DAFF"))
  42. # order samples by group
  43. boxplot(Data[,ord], boxwex=0.6, notch=F, main="boxplot", outline=FALSE, las=2, col=gs[ord])
  44. legend("topright",groups, fill=palette(), bty="n")
  45. #scatterplot
  46. pairs(~mock+infected,data = Data,main = "Scatterplot Matrix",pch=20,col="#FCBDBD")
  47. #Mock_Infected scatterplot
  48. plot(mock,infected,xlab = "infected",ylab = "mock",pch=20,col="#F1A78D"
  49.      ,cex=1, main="Mock_Infected scatterplot" )
  50.  
  51.  
Success #stdin #stdout #stderr 0.24s 38360KB
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Error in library(GEOquery) : there is no package called ‘GEOquery’
Execution halted
https://ideone.com/mnQBZP
language:
R (R 3.5.2)
created:
3 years ago
visibility:
secret

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