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Question: GEO error : Warning message: In read.table(file = file, header = header, sep = sep, quote = quote, : not all columns named in 'colClasses' exist
1
gravatar for cynthiak14
2.3 years ago by
cynthiak1410
cynthiak1410 wrote:

I tried retrieving a data from NCBI GEO using Rstudio.

The download was complete as the following was shown.

> gset <- getGEO("GSE30565", GSEMatrix =TRUE, destdir= "C:/Documents and Settings/Administrator/My Documents/Downloads", AnnotGPL=FALSE)
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30565/matrix/
Found 1 file(s)
GSE30565_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30565/matrix/GSE30565_series_matrix.txt.gz'
downloaded 792 KB

File stored at: 
C:/Documents and Settings/Administrator/My Documents/Downloads/GPL13884.soft

 

But what worries me is the warning line following this :

Warning message:
In read.table(file = file, header = header, sep = sep, quote = quote,  :
  not all columns named in 'colClasses' exist

I am sure that my Rstudio is uptodate including the packages:

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows XP (build 2600) Service Pack 3

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

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

other attached packages:
[1] GEOquery_2.38.4     Biobase_2.32.0      BiocGenerics_0.18.0

loaded via a namespace (and not attached):
[1] httr_1.2.1     R6_2.1.3       tools_3.3.1    RCurl_1.95-4.8 bitops_1.0-6  
[6] XML_3.98-1.4 

 

Kindly check if there is a bug in the package or tell me what i should do to sort this warning.

ADD COMMENTlink modified 2.3 years ago by Sean Davis21k • written 2.3 years ago by cynthiak1410
0
gravatar for Sean Davis
2.3 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

This is a known issue that I need to clean up.  You can safely ignore this warning.  Sorry about the confusing message.

ADD COMMENTlink written 2.3 years ago by Sean Davis21k
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