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seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
http://seandavi.github.io/GEOquery/
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AnnotatedDataFrame 'initialize' could not update varMetadata #98

Open khughitt opened 4 years ago

khughitt commented 4 years ago

Came across another problematic GEO dataset I thought I would report (GSE136400):

Code to reproduce:

library(GEOquery)
getGEO('GSE136400')

Output / Error message:

Found 1 file(s)                                                                                                                         
GSE136400_series_matrix.txt.gz                                                                                                          
Using locally cached version: /data/human/geo/GSE136400/raw/GSE136400_series_matrix.txt.gz                                              
Parsed with column specification:                                                                                                       
cols(                                                                                                                                   
  .default = col_double(),                                                                                                              
  ID_REF = col_character()                                                                                                              
)                                                                                                                                       
See spec(...) for full column specifications.                                                                                           
|=======================================================================================================================================
Error in value[[3L]](cond) :                                                                                                            
  duplicate row.names: CXXC1, CXXC1P1, CXXC4, CXXC5                                                                                     
  AnnotatedDataFrame 'initialize' could not update varMetadata:                                                                         
  perhaps pData and varMetadata are inconsistent?                                                                                       
Calls: getGEO ... parseGSEMatrix -> new -> initialize -> initialize -> .local -> tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>