Hi, Is there any way to retrieve ChIP seq data from GEO data base. Some publishers have posted the processed data in the supplementary file which is easy to retrieve. However, some such as GSE32222 have not while they have the raw data in the supplementary. How can I retrieve the available processed data from this entry since the instruction on GEOquery package does not apply on ChIPseq data as below:
library(GEOquery)
GSE32222 <- getGEO("GSE32222", GSEMatrix = FALSE) gsmplatforms <- lapply(GSMList(GSE32222),function(x) {Meta(x)$platform_id})
gsmlist = Filter(function(GSE32222) {Meta(GSE32222)$platform_id=='GPL10999'},GSMList(GSE32222)) length(gsmlist) head(gsmlist)
ID <- Table(GPLList(GSE32222)[[1]])$ID ID
NULL
Table(GPLList(GSE32222)[[1]])
data frame with 0 columns and 0 rows
data.matrix <- do.call('cbind',lapply(gsmlist,function(x) {tab <- Table(x) mymatch <- match(ID,tab$ID) return(tab$VALUE[mymatch]) })) data.matrix <- apply(data.matrix,2,function(x) {as.numeric(as.character(x))})
Thanks for help!
