Question: GEOquery problems while trying to process GSE soft files
0
gravatar for sz
4.2 years ago by
sz0
United Kingdom
sz0 wrote:

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 • 726 views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by sz0
Answer: GEOquery problems while trying to process GSE soft files
0
gravatar for James W. MacDonald
4.2 years ago by
United States
James W. MacDonald52k wrote:

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)

 

 

ADD COMMENTlink written 4.2 years ago by James W. MacDonald52k
Answer: GEOquery problems while trying to process GSE soft files
0
gravatar for sz
4.2 years ago by
sz0
United Kingdom
sz0 wrote:

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

ADD COMMENTlink written 4.2 years ago by sz0

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
                                 Dload  Upload   Total   Spent    Left  Speed
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)
  varMetadata: labelDescription
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.

ADD REPLYlink written 4.2 years ago by James W. MacDonald52k
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