Question: GEOquery:Get error sampleNames
1
gravatar for ustcxyf
6 months ago by
ustcxyf10
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:

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

 

output:

$`GSE2553_series_matrix.txt.gz`
ExpressionSet (storageMode: lockedEnvironment)
assayData: 12599 features, 181 samples 
  element names: exprs 
protocolData: none
phenoData
  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
featureData
  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

 

locale:

[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 • 238 views
ADD COMMENTlink modified 5 months ago by Bioconductor Community ♦♦ 0 • written 6 months ago by ustcxyf10
2

 

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 https://github.com/seandavi/GEOquery/issues/74

ADD REPLYlink written 6 months ago by Jinsong Zhang60

Yes, the "bug" here is a change in behavior of read_tsv and friends in readr. See https://github.com/tidyverse/readr/issues/925

ADD REPLYlink written 6 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 6 months ago by Sean Davis21k

Looks like a bug to me. I filed an issue (https://github.com/seandavi/GEOquery/issues/75)

ADD REPLYlink modified 6 months ago • written 6 months ago by Sean Davis21k
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