QCcheck

Normal Tissue Panel

library(arrayQualityMetrics)

## Warning: multiple methods tables found for 'unlist'

## Warning: multiple methods tables found for 'as.vector'

## Warning: multiple methods tables found for 'unlist'

## Warning: multiple methods tables found for 'as.vector'

## Warning: multiple methods tables found for 'unlist'

## Warning: multiple methods tables found for 'unlist'

library(Biobase)
library(angelare)
data(normal.prot.eset)
data(normal.mrna.eset)
##normal.prot = as.matrix(read.delim("24870543_ST6_prot.txt", row.names = 1))
##normal.mrna = as.matrix(read.delim("24870543_ST6_mRNA.txt", row.names = 1))

Scaling, imputation etc

prepDat <- function(eset){
  exprs(eset) <- t(scale(t(exprs(eset))))
  eset
}
normal.prot.eset=prepDat(normal.prot.eset)
normal.mrna.eset=prepDat(normal.mrna.eset)

#normal.prot.eset=ExpressionSet(normal.prot)
arrayQualityMetrics(normal.prot.eset, force=TRUE)

## The directory 'arrayQualityMetrics report for normal.prot.eset' has been created.

## (loaded the KernSmooth namespace)

#normal.mrna.eset=ExpressionSet(normal.mrna)
arrayQualityMetrics(normal.mrna.eset, force=TRUE)

## The directory 'arrayQualityMetrics report for normal.mrna.eset' has been created.

Correlation heatmap for mRNA:

normal.mrna.cor=cor(exprs(normal.mrna.eset), use="complete.obs")
library(pheatmap)
diag(normal.mrna.cor)=NA
pheatmap(normal.mrna.cor)

Correlation heatmap for protein:

normal.prot.cor=cor(exprs(normal.prot.eset), use="complete.obs")
diag(normal.prot.cor)=NA
pheatmap(normal.prot.cor)

NCI-60 Panel

library(SummarizedExperiment)
data(nci60.mrna.eset)
data(nci60.prot.eset)
nci60.prot.eset=prepDat(nci60.prot.eset)
nci60.mrna.eset=prepDat(nci60.mrna.eset)
#load("NCI60.summarizedExperimentiBAQ.rda")
#nci60.mrna = sset@assays[[1]]
#nci60.prot = sset@assays[[2]]

nzeros = apply(nci60.prot, 1, function(x) sum(x==0))
nci60.prot = nci60.prot[nzeros <= 5, ]

#nci60.prot.eset=ExpressionSet(nci60.prot)
arrayQualityMetrics(nci60.prot.eset, force=TRUE)

## The report will be written into directory 'arrayQualityMetrics report for nci60.prot.eset'.

#nci60.mrna.eset=ExpressionSet(nci60.mrna)
arrayQualityMetrics(nci60.mrna.eset, force=TRUE)

## The report will be written into directory 'arrayQualityMetrics report for nci60.mrna.eset'.

Correlation heatmap for mRNA:

nci60.mrna.cor=cor(exprs(nci60.mrna.eset), use="complete.obs")
diag(nci60.mrna.cor)=NA
pheatmap(nci60.mrna.cor)

Correlation heatmap for protein:

nci60.prot.cor=cor(exprs(nci60.prot.eset), use="complete.obs")
diag(nci60.prot.cor)=NA
pheatmap(nci60.prot.cor)

hist(normal.prot.cor)

hist(nci60.prot.cor)

hist(normal.mrna.cor)

hist(nci60.mrna.cor)