Question

assayData: 0 features

0

Entering edit mode

Ed Siefker ▴ 230

@ed-siefker-5136

Last seen 13 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 • 4.0k views

ADD COMMENT • link updated 3.8 years ago by H. Z. Amini ▴ 10 • written 9.3 years ago by Ed Siefker ▴ 230

score 0 · Answer 1 · 2015-09-16

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 days 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.

ADD COMMENT • link 9.3 years ago James W. MacDonald 67k

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

ADD REPLY • link 9.3 years ago Ed Siefker ▴ 230

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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.

ADD REPLY • link 9.3 years ago James W. MacDonald 67k

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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.

ADD REPLY • link 3.8 years ago H. Z. Amini ▴ 10

score 0 · Answer 2 · 2021-02-26

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Entering edit mode

H. Z. Amini ▴ 10

@habibolla-24859

Last seen 3.4 years 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.

ADD COMMENT • link 3.8 years ago H. Z. Amini ▴ 10