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Question: GEOQuery - Encoding UTF-8
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gravatar for Adrian Johnson
15 months ago by
Adrian Johnson330 wrote:

Hello:

I am trying to download GSE data tables and encountered the following error. 

I cannot find a proper solution. Could someone help. 

 

Thanks

Adrian

 

 

> GSE2034_clindata=getGSEDataTables("GSE2034")
No encoding supplied: defaulting to UTF-8.
Error in UseMethod("xpathApply") : 
  no applicable method for 'xpathApply' applied to an object of class "NULL"
In addition: Warning message:
In xmlRoot.XMLInternalDocument(xmlParseDoc(txt)) : empty XML document

 

 

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 8.1 x64 (build 9600)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] hgu133ahsentrezg.db_20.0.0   org.Hs.eg.db_3.3.0           hgu133ahsentrezgprobe_20.0.0 hgu133ahsentrezgcdf_20.0.0   AnnotationDbi_1.34.4        
 [6] IRanges_2.6.1                S4Vectors_0.10.2             gcrma_2.44.0                 affy_1.50.0                  GEOquery_2.38.4             
[11] Biobase_2.32.0               BiocGenerics_0.18.0          BiocInstaller_1.22.3        

loaded via a namespace (and not attached):
 [1] XVector_0.12.1        splines_3.3.1         zlibbioc_1.18.0       R6_2.1.2              httr_1.2.1            tools_3.3.1           DBI_0.5              
 [8] preprocessCore_1.34.0 affyio_1.42.0         bitops_1.0-6          curl_1.2              RCurl_1.95-4.8        RSQLite_1.0.0         Biostrings_2.40.2    
[15] XML_3.98-1.4         

 

ADD COMMENTlink written 15 months ago by Adrian Johnson330
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