Question: GEOquery:Get error sampleNames
gravatar for ustcxyf
11 months ago by
ustcxyf10 wrote:

Hello everyone,

I run the exmaple in GEOquery documentation but there are some errors. I can't get correct sampleNames.

I have tried several different datasets and all get error.But my friend use  older versions can get same result wtih documentation.I think there are some problem in my R enviroment.

Is this an problem in the GEOquery or my fault ?


my code:

gsm <- getGEO("GSE2553", GSEMatrix=TRUE)



ExpressionSet (storageMode: lockedEnvironment)
assayData: 12599 features, 181 samples 
  element names: exprs 
protocolData: none
  sampleNames: 0.2701103 0.3925373 ... 1.4989663 (181 total)   #error  The correct output is  GSM48681 GSM48682 ...

  varLabels: title geo_accession ... data_row_count (30 total)
  varMetadata: labelDescription
  featureNames: 2 3 ... NA.10693 (12599 total) 
  fvarLabels: ID PenAt ... Chimeric_Cluster_IDs (13 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL1977


> sessionInfo()

R version 3.5.1 (2018-07-02)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows >= 8 x64 (build 9200)


Matrix products: default



[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   

[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                             

[5] LC_TIME=Chinese (Simplified)_China.936   


attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     


other attached packages:

[1] GEOquery_2.50.0     Biobase_2.42.0      BiocGenerics_0.28.0


loaded via a namespace (and not attached):

 [1] Rcpp_1.0.0         tidyr_0.8.2        crayon_1.3.4       dplyr_0.7.8        assertthat_0.2.0   R6_2.3.0         

 [7] magrittr_1.5       pillar_1.3.0       rlang_0.3.0.1      curl_3.2           bindrcpp_0.2.2     limma_3.38.2     

[13] xml2_1.2.0         tools_3.5.1        readr_1.2.1        glue_1.3.0         purrr_0.2.5        hms_0.4.2         

[19] compiler_3.5.1     pkgconfig_2.0.2    BiocManager_1.30.4 tidyselect_0.2.5   bindr_0.1.1        tibble_1.4.2 

geoquery • 356 views
ADD COMMENTlink modified 10 months ago by Bioconductor Community ♦♦ 0 • written 11 months ago by ustcxyf10


I encountered the exact same problem a week ago. After spending some time, I found that downgrading the "reader" from 1.2.1 to 1.1.1 would temporarily solve the problem. see

ADD REPLYlink written 11 months ago by Jinsong Zhang60

Yes, the "bug" here is a change in behavior of read_tsv and friends in readr. See

ADD REPLYlink written 11 months ago by Sean Davis21k

Just a quick update--the Rstudio team has a working fix and it is going through code review. Once that is completed and the new readr package is released, the GEOquery problem will be resolved. 

ADD REPLYlink written 11 months ago by Sean Davis21k

Looks like a bug to me. I filed an issue (

ADD REPLYlink modified 11 months ago • written 11 months ago by Sean Davis21k
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