GEOquery: 0 features in the gset object
1
2
Entering edit mode
alakatos ▴ 110
@alakatos-6983
Last seen 19 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.

Would you please advise how to adjust my code for this dataset?

Thank you for your help.

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)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: GPL18573 

  

geoquery • 1.8k views
ADD COMMENT
3
Entering edit mode
@sean-davis-490
Last seen 3 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.

 

ADD COMMENT
0
Entering edit mode

Thank you for your reply.

Anita

ADD REPLY
0
Entering edit mode

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?

Appreciate your help.

ADD REPLY

Login before adding your answer.

Traffic: 347 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6