Question: Nimblegen DMA methylation microarray data analysis
0
gravatar for Explorer
3.4 years ago by
Explorer70
Australia
Explorer70 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 • 998 views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Explorer70
1
gravatar for Shicheng Guo
3.4 years ago by
Shicheng Guo7.7k
Shicheng Guo7.7k 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 3.4 years ago • written 3.4 years ago by Shicheng Guo7.7k
0
gravatar for Explorer
3.4 years ago by
Explorer70
Australia
Explorer70 wrote:

Cant find the package GEOquery.

ADD COMMENTlink written 3.4 years ago by Explorer70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1852 users visited in the last hour