Question: Nimblegen DMA methylation microarray data analysis
0
gravatar for EpiExplorer
4.3 years ago by
EpiExplorer70
New Zealand
EpiExplorer70 wrote:

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.

microarray • 1.2k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by EpiExplorer70
1
gravatar for Shicheng Guo
4.3 years ago by
Shicheng Guo8.3k
Shicheng Guo8.3k wrote:

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]]))
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Shicheng Guo8.3k
0
gravatar for EpiExplorer
4.3 years ago by
EpiExplorer70
New Zealand
EpiExplorer70 wrote:

Cant find the package GEOquery.

ADD COMMENTlink written 4.3 years ago by EpiExplorer70
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