Data frame with 0 columns and 0 rows
0
0
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@626d4e88
Last seen 3 days ago
Japan

Dear All,

I was trying to retrieve a GSE record from NCBI GEO using GEOquery package following the introduction like

gse <- getGEO("GSE152382",GSEMatrix=FALSE)

head(Meta(gse))

names(GSMList(gse))

GSMList(gse)[[1]]

result of the first three steps are just similar to that shown in the "Using the GEOquery Package"

but for the last step


GSMList(gse)[[1]]

where supposed to show the data I need like

An object of class "GEODataTable" ** Column Descriptions ** Column 1
2 VALUE 3 ABS_CALL Description 1 ID_REF = 2 MAS 5.0 Statistical Algorithm (mean scaled to 500) 3 MAS 5.0 Absent, Marginal, Present call with Alpha1 = 0.05, Alpha2 = 0.065 ** Data Table ** ID_REF VALUE ABS_CALL 1 AFFX-BioB-5_at 953.9 P 2 AFFX-BioB-M_at 2982.8 P 3 AFFX-BioB-3_at 1657.9 P 4 AFFX-BioC-5_at 2652.7 P 5 AFFX-BioC-3_at 2019.5 P 22278 more rows ...

my result turned to be

An object of class "GEODataTable" ** Column Descriptions ** [1] Column Description <0 rows> (or 0-length row.names) ** Data Table ** data frame with 0 columns and 0 rows

I also tried


gse152382<- getGEO('GSE152382',GSEMatrix=TRUE)
show(gse152382)

it showed

$GSE152382_series_matrix.txt.gz ExpressionSet (storageMode: lockedEnvironment) assayData: 0 features, 192 samples
element names: exprs
protocolData: none phenoData sampleNames: GSM4613909 GSM4613910 ... GSM4614100 (192 total) varLabels: title geo_accession ... strain:ch1 (46 total) varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' pubMedIds: 32901092 Annotation: GPL17021

and I still don't know where to find the data, what am I missing?

Thanks!

GEOquery • 133 views
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It seems there is no expression data available in your record but you may be able download processed data with getGEOSuppFiles() according to GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152382

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