Nimblegen DMA methylation microarray data analysis

Question

[EpiExplorer]

Hi, I would like to know what are the tools available- R packages or GUI based, for DNA methylation microarray analysis.

I would like to import and analyze the publicly available dataset GSE57971 which is from NimbleGen Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array platform.

Please help me with this.

PS: I tried CHARM and MEDEP but the documentation isn't great.

Thanks for your time and help.

Answer 1

[Shicheng Guo]

You can do it by yourself one by one with differential methylation test and FDR and further bioinforamtics analysis.

# GSE52271
source("http://bioconductor.org/biocLite.R")
biocLite("GEOquery")
library("GEOquery")
GSE57971 <- getGEO("GSE57971")
data <- as.data.frame(exprs(GSE57971[[1]]))
phen <- pData(phenoData(GSE57971[[1]]))

Answer 2

[EpiExplorer]

Cant find the package GEOquery.