Dear all, It's the first time that I move to analyze methylated data. I will start with the dataset https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96067, containing data extracted from Agilent-023795 Human DNA Methylation Microarray 244k (Probe Name Version). My goal is to look for differentially methylated regions and related genes. Please, can someone suggest me which package will be suitable for my scope? Any suggest is welcome. Thank you guys. Emilio
On the page to which you link, click on the blue button called Analyze with GEO2R. Then, click on the R script tab and execute the code that appears. That will, more than likely, give you the normalised beta methylation values (check via boxplot). With those, you can do the differential methylation analysis.
library(Biobase) library(GEOquery) # load series and platform data from GEO gset <- getGEO("GSE96067", GSEMatrix =TRUE, getGPL=FALSE) if (length(gset) > 1) idx <- grep("GPL19930", attr(gset, "names")) else idx <- 1 gset <- gset[[idx]] # set parameters and draw the plot dev.new(width=4+dim(gset)[]/5, height=6) par(mar=c(2+round(max(nchar(sampleNames(gset)))/2),4,2,1)) title <- paste ("GSE96067", '/', annotation(gset), " selected samples", sep ='') boxplot(exprs(gset), boxwex=0.7, notch=T, main=title, outline=FALSE, las=2)