Entering edit mode
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_se
ries_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_se
ries_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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