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I'm working for a project using GEO, in order to analyze some gene expression data. The SuperSeries I am referring to is GSE73304, but I found some problems working on the SubSeries GSE73303.

I started my analysis Microarray expression dataset and everything was fine. Now I have to investigate the other dataset, the one target as Bisulfite-Seq. But when I try to see inside it, I find there are correctly 20 patients, but 0 features, so seems it is empty. I attach R output:

library(GEOquery)
gsemet <- getGEO("GSE73303")

> gsemet
$GSE73303_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 20 samples 
element names: exprs 
protocolData: none
phenoData
sampleNames: GSM1890515 GSM1890516 ... GSM1890534 (20 total)
varLabels: title geo_accession ... Sex:ch1 (44 total)
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
pubMedIds: 27437034
28883895 
Annotation: GPL11154 

Could someone help me to find where I'm wrong? Or maybe, if the file is empty, pass me the right file?

Thank you very much in advance

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1 Answer 1

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It's NGS data, while GEOquery only returns data for arrays. You will either need to use the data they provude in the supplement of the GEO submission (if they do, it's not mandatory), or download and process fastq from scratch.

It's not gene expression by the way, it's methylation data, bisulfite sequencing.

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