you have noted that getGEO returns a list, and the first element of the list
you got is an ExpressionSet instance.

you are asking about access to the assayData.  This concerns ExpressionSet
mechanics, not GEOquery

> library(Biobase)

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

> data(sample.ExpressionSet)
> assayData(sample.ExpressionSet)
<environment: 0x100b1eb40>
> ls(.Last.value)
[1] "exprs"    "se.exprs"
> dim(assayData(sample.ExpressionSet)$exprs)
[1] 500  26
> dim(assayData(sample.ExpressionSet)$se.exprs)
[1] 500  26
> dim(exprs(sample.ExpressionSet))
[1] 500  26

assayData is not intended for direct handling by end users.  the exprs()
method will retrieve the matrix of expression
values.


On Tue, Aug 16, 2011 at 7:20 AM, <J.delasHeras@ed.ac.uk> 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)
>>
> [1] "list"
>
>> length(u)
>>
> [1] 1
>
>  class(u[[1]])
>>
> [1] "ExpressionSet"
> attr(,"package")
> [1] "Biobase"
>
> ok, so I rename that, and look at its structure:
>
> eset<-u[[1]]
> 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@phenoData@data #samples
> eset@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@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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