GEOquery problems while trying to process GSE soft files
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sz • 0
@sz-8955
Last seen 6.6 years ago
United Kingdom

I am trying to capture GSE60701 GEOquery and am running up against the following n message:

could not find function"get GEO

What does that mean?  I used

gse <- getGEO(filename=system.file("extdata/GSE60701_family.soft.gz,package="GEOquery"))

and get that message.

Any thoughts?

GSE soft files GEO data • 1.1k views
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@james-w-macdonald-5106
Last seen 1 day ago
United States

Any time you see a message that says 'Could not find function', it means that you haven't loaded the package that contains that function yet. So start with

library(GEOquery)

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sz • 0
@sz-8955
Last seen 6.6 years ago
United Kingdom

James  Thanks...not sure what to do after that!!!

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Just run the code. But you shouldn't ever be calling system.file(). That is something people do in vignettes when they want to show how to do something that might only work 'normally' in an interactive session, or when there is an internet connection. So say you want GSE60701, for real.

> library(GEOquery)
> z <- getGEO("GSE60701")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60701/matrix/
Found 1 file(s)
GSE60701_series_matrix.txt.gz
% Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
100  4302  100  4302    0     0   3026      0  0:00:01  0:00:01 --:--:--  3027
File stored at:
/data3/tmp/Rtmp2k3GiT/GPL13112.soft
> z[[1]]
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 12 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM1486081 GSM1486082 ... GSM1486092 (12 total)
varLabels: title geo_accession ... supplementary_file_1 (42 total)
featureData: none
experimentData: use 'experimentData(object)'
Annotation: GPL13112

And then you can do whatever analysis you might want. But do note that getGEO() returns a list, so depending on the GSE you download, you may get one or more list items. If that doesn't mean anything to you, then read 'An Introduction to R', because you will need it.