GEOquery: 0 features in the gset object
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alakatos ▴ 110
@alakatos-6983
Last seen 24 months ago
United States

Hello All,

I have  been downloading  GSE sets from GEO. This time I tried to download  RNAseq data packaged as GSE. Unfortunately, the code I have been using produced empty file.

Anita

gset <- getGEO("GSE67835", GSEMatrix =TRUE)
if (length(gset) > 1) idx <- grep("GPL18573", attr(gset, "names")) else idx <- 1
gset67835 <- gset[[idx]]
gset67835
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 328 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM1657871 GSM1657872 ... GSM1658366 (328 total)
varLabels: title geo_accession ... supplementary_file_2 (44 total)
featureData: none
experimentData: use 'experimentData(object)'
Annotation: GPL18573 

geoquery • 2.1k views
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@sean-davis-490
Last seen 15 days ago
United States

Unfortunately, it appears that the submitters did not submit the data into GEO.  Instead, the data were actually submitted as .txt files, one per sample.  This means that it will be extra work for you to load this dataset and the approach for doing so is not something that is easily standardized.  GEOquery can help you get started:

getGEOSuppFiles('GSE67835')

This will download GSE67835_Raw.tar which you can untar, resulting in one file per sample.  You can then read these files into R one-at-a-time and attach the data to the existing ExpressionSet.

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Anita

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Thank you for the hint. Would you please explain me more how to do the process? Actually I'm very new in this BIOdata field and I dont know exactly what to do. For my data (GSE81540), I dont have "_Raw.tar" part in the GEO website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81540

So I'm wondering what should I do?