On Mon, Feb 28, 2011 at 12:14 AM, Kridsadakorn Chaichoompu <
kridsadakorn.cha@biotec.or.th> wrote:

> Dear Sean Davis,
>
> Thank you very much. It works!
>
> I'm not quite familiar with R. Could I ask you the stupid question?
>
> > show(gse)
> $GSE2553_series_matrix.txt.gz
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 12600 features, 181 samples
>   element names: exprs
> protocolData: none
> phenoData
>   sampleNames: GSM48681, GSM48682, ..., GSM48861  (181 total)
>   varLabels and varMetadata description:
>     title: NA
>     geo_accession: NA
>     ...: ...
>     data_row_count: NA
>     (30 total)
> featureData
>   featureNames: 1, 2, ..., 12600  (12600 total)
>   fvarLabels and fvarMetadata description:
>     ID: NA
>     PenAt: NA
>     ...: ...
>     Chimeric_Cluster_IDs: NA
>     (13 total)
>   additional fvarMetadata: Column, Description
> experimentData: use 'experimentData(object)'
> Annotation: GPL1977
>
> I don't know how to access this data structure.
> How could I access each features such as  the information of GSE object and
> the information of each sample?
>
>
Hi, Kridsadakom.

This is a list of ExpressionSets, though in this case there is only one
member of the list.  To access the first and only ExpressionSet, you can do:

gse[[1]]

The Biobase package defines the ExpressionSet class, so reading the
vignettes associated with that package will be helpful.  To get a glimpse,
though, try:

head(pData(gse[[1]]))
head(fData(gse[[1]]))
head(exprs(gse[[1]]))

Sean



> Thank you very much for the following reply.
>
> Kridsadakorn
>
> On Feb 25, 2011, at 7:06 PM, Sean Davis wrote:
>
>
>
> On Fri, Feb 25, 2011 at 2:38 AM, Kridsadakorn Chaichoompu <
> kridsadakorn.cha@biotec.or.th> wrote:
>
>> Dear Sean Davis,
>>
>> I'm interesting to use GEOQuery to get the data from GEO, I think it's
>> very good package.
>>
>> I installed GEOQuery package on my machine, Linux, then tried to follow
>> the tutorial, in section 4.1
>> However, I got the error as follow
>>
>> > gse <- getGEO("GSE2553", GSEMatrix = TRUE)
>> Found 1 file(s)
>> GSE2553_series_matrix.txt.gz
>> trying URL '
>> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2553/GSE2553_series_matrix.txt.gz
>> '
>> Error in download.file(sprintf("
>> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/%s/%s",  :
>>  cannot open URL '
>> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2553/GSE2553_series_matrix.txt.gz
>> '
>>
>> I copied the url to the browser to check if the file is still in the GEO
>> server; yes it is.
>> I just want to know the reason why I got this error.
>>
>> I'm using Bioconductor 2.7, Ubuntu.  wget and curl already were installed.
>>
>>
> Try:
>
> options('download.file.method'='curl')
>
> And then retry the getGEO call.  Let me know if that doesn't work for you.
>
> Sean
>
>
>> Thank you very much for the following reply
>>
>> Regards,
>>
>> Kridsadakorn Chaichoompu
>> Biostatistics & Informatics Lab.
>> Genome Institute, BIOTEC
>> 113 Thailand Science Park
>> Phaholyothin Road, Klong 1
>> Klong Luang, Phathumthani
>> Thailand 12120
>>
>> kridsadakorn.cha@biotec.or.th
>> +662 564 7000 ext 5552
>>
>>
>
>

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