Question: Analysing GSE datasets with GEOquery
0
gravatar for IsmailM
2.8 years ago by
IsmailM110
UK/London/University College London
IsmailM110 wrote:

Hi,

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 GSE61369 etc.

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

enter image description here

GEO data series that isn't working enter image description here

I would appreciate any help in getting the above code working with the following accesion number: GSE61369.

rna-seq R geo • 2.4k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by IsmailM110

GSE61369 is all sequencing data; I don't think sequencing studies have been summarised as expression matrices by GEO

ADD REPLYlink written 2.8 years ago by russhh5.2k
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