Retrieving ChIP-seq data from Geo database
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poodap127 • 0
@poodap127-22951
Last seen 19 months ago

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!

ChIPseq GEO data base • 186 views
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@james-w-macdonald-5106
Last seen 8 hours ago
United States

You could use getGEOSuppFiles

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