Search
Question: GEOquery::getGEO warning: not all columns named in 'colClasses' exist
0
gravatar for alexvpickering
18 months ago by
alexvpickering80 wrote:

I'm getting a warning message from GEOquery function getGEO (only seems to happen with GSEMatrix = TRUE).  May be a bug (I believe everything is up to date).

library(GEOquery)
gse <- getGEO("GSE61538", GSEMatrix=TRUE)

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

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
[1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8      
[4] LC_COLLATE=en_CA.UTF-8     LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8  
[7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                  LC_ADDRESS=C             
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

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_1.1.0     R6_2.1.2       tools_3.3.0    RCurl_1.95-4.8 bitops_1.0-6   XML_3.98-1.4  
ADD COMMENTlink modified 18 months ago by Sean Davis21k • written 18 months ago by alexvpickering80
2
gravatar for Sean Davis
18 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:
I need to do a little cleanup, but this is just a warning and will not affect your ability to use GEOquery.
ADD COMMENTlink written 18 months ago by Sean Davis21k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 229 users visited in the last hour