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gravatar for Sean Davis
7.7 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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 >> >> > > [[alternative HTML version deleted]]
ADD COMMENTlink written 7.7 years ago by Sean Davis21k
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