I'm having difficulties in analyzing a number of GSE datasets using the GEOquery package.
I have managed to get it to work with certain accession numbers, but am having issues running the same code with other accession numbers.
e.g. it works with
GSE51808 but does not work with
accession <- 'GSE51808' # accession <- 'GSE61369' # DOES NOT WORK gset <- getGEO(accession, GSEMatrix = TRUE) if (length(gset) > 1) idx <- grep(gset@annotation, attr(gse, "names")) else idx <- 1 eset <- gset[[idx]] X <- exprs(eset) # Get Expression Data pData <- pData(eset) gene.names <- as.character(eset@featureData@data[, "Gene Symbol"]) rownames(X) <- gene.names head(X)
It seems that both datasets are downloaded from NCBI via the
getGEO() command but the matrix is not created with the second datasets meaning that the downstream analysis fails...
GEO data series that is working
GEO data series that isn't working
I would appreciate any help in getting the above code working with the following accesion number: