assayData: 0 features
2
0
Entering edit mode
Ed Siefker ▴ 230
@ed-siefker-5136
Last seen 9 months ago
United States

Using GEOquery, I'm not getting any features and a lot of the
methods don't work.  What am I doing wrong?

> gse <- getGEO("GSE48206")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48206/matrix/
Found 1 file(s)
GSE48206_series_matrix.txt.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  2325  100  2325    0     0   2660      0 --:--:-- --:--:-- --:--:--  2663
Using locally cached version of GPL16417 found here:
/tmp/Rtmp49zUTd/GPL16417.soft
> show(gse)
$GSE48206_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 6 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM1172734 GSM1172735 ... GSM1172739 (6 total)
  varLabels: title geo_accession ... supplementary_file_2 (45 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: GPL16417

> head(Meta(gse))
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘Meta’ for signature ‘"list"’
> names(GSMList(gse))
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘GSMList’ for
signature ‘"list"’

geoquery • 1.1k views
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@james-w-macdonald-5106
Last seen 21 hours ago
United States

You aren't looking at the GEO website to see if normalized data are available, which in this case they aren't. You can get the raw data using getGEOSuppFiles(), but it's not really raw data - instead they supply TPM values from RSEM. I don't believe there is a pipeline for dealing with these data from within GEOquery, so you may need to 'roll your own' functions.

Alternatively you can get the .sra files from SRA and re-align if you need counts/gene.

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How do I tell from the GEO website whether count data is directly available through GEOquery?

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Ah, good question. It does actually look like there is a series matrix file available. But if you click on the link, you can see on the FTP site that it is only 3 kb. But in general, if there is a link to the SRA, then you know it's RNA-Seq data, and submitters can either upload a series matrix of counts/TPM/RPKM/whatever, or they can upload individual files. At that point you have to look closer to see what they uploaded, and in what format.

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Thank you for the thought. Would you please explain me more how to do it in Rsudio? Specifically for my data (GSE81540).

Appreciate your help.

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H. Zadeh • 0
@habibolla-24859
Last seen 3 days ago
Morgantown

Thank you for the thought. Would you please explain me more how to do it in Rsudio? Specifically for my data (GSE81540).

Appreciate your help.

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