Question: GEOquery: how to extract experimental data? (confused)
8.3 years ago by
J.delasHeras@ed.ac.uk • 1.9k
J.delasHeras@ed.ac.uk • 1.9k wrote:
I have been until now downloading GEO data directly to my computer and using basic R functions to load tables and process them. It works, but I figured I would probably save time if I learn to use the GEOquery package, which looks promising. However, I'm failing tremendously at my first attempt. I can get a lot of good information, except the actual experiment data... and it seems to be there, but can't get to it! Example. I'm trying to get GSE19044, which contains 42 samples and uses the Illumina WG6 platform, which is great as I'm familiar with it. so I do: library(GEOquery) u = getGEO('GSE19044') show(u) > show(u) $GSE19044_series_matrix.txt.gz ExpressionSet (storageMode: lockedEnvironment) assayData: 45281 features, 42 samples element names: exprs protocolData: none phenoData sampleNames: GSM471318, GSM471319, ..., GSM471359 (42 total) varLabels and varMetadata description: title: NA geo_accession: NA ...: ... data_row_count: NA (39 total) featureData featureNames: ILMN_1212602, ILMN_1212603, ..., ILMN_3163582 (45281 total) fvarLabels and fvarMetadata description: ID: NA Species: NA ...: ... SPOT_ID: NA (31 total) additional fvarMetadata: Column, Description experimentData: use 'experimentData(object)' Annotation: GPL6887 It looks good. It looks like what I want is the 'assayData'. But I can't get to it. 'u' is a list, containing one element... > class(u)  "list" > length(u)  1 > class(u[])  "ExpressionSet" attr(,"package")  "Biobase" ok, so I rename that, and look at its structure: eset<-u[] str(eset) > str(eset) Formal class 'ExpressionSet' [package "Biobase"] with 7 slots ..@ assayData :<environment: 0x0645ec5c=""> ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] [...] (omitted for brevity) I can extract the sample names, the basic annotation/probe identity etc easily: eset at phenoData@data #samples eset at featureData@data #annotation but how do I get into 'assayData'? from the 'show(u)' it looks like it contains what I am after: 45281 features, 42 samples ... but it's class 'environment' and that's throwing me off. I was looking into the GEOquery user guide, but I'm still none the wiser. How do I get in there? thanks for any help. Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507090 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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