GEOquery getGEO 404
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anthony.nash ▴ 20
@anthonynash-14843
Last seen 10 months ago
University of Oxford

I would appreciate a little help with a GEOquery issue. I've been able to view the gene set of interest on GEO NCBI website (GSE53764), however, the R code required for more in-depth analysis is failing at the first step. 

# Version info: R 3.2.3, Biobase 2.30.0, GEOquery 2.40.0, limma 3.26.8
# R scripts generated  Tue Jan 23 03:22:20 EST 2018
################################################################
#   Differential expression analysis with limma
library(Biobase)
library(GEOquery)
library(limma)

# load series and platform data from GEO
gset <- getGEO("GSE53764", GSEMatrix =TRUE, AnnotGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL6543", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53764/matrix/
OK
Found 2 file(s)
/geo/series/GSE53nnn/GSE53764/
downloaded 0 bytes

Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  : 
  cannot download all files
In addition: Warning message:
In download.file(
sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  :
  URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53764/matrix//geo/series/GSE53nnn/GSE53764/': status was '404 Not Found'

My R sessionInfo:

R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] BiocInstaller_1.24.0 limma_3.30.13        GEOquery_2.40.0      Biobase_2.34.0      
[5] BiocGenerics_0.20.0  JPSurv_1.0.1         vioplot_0.2          sm_2.2-5.4          

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15     XML_3.98-1.9     bitops_1.0-6     R6_2.2.2         grid_3.3.3      
 [6] plyr_1.8.4       gtable_0.2.0     scales_0.5.0     httr_1.3.1       ggplot2_2.2.1   
[11] rlang_0.1.6      lazyeval_0.2.1   tools_3.3.3      RCurl_1.95-4.10  munsell_0.4.3   
[16] colorspace_1.3-2 tibble_1.4.1  

I downloaded the geneset files myself, there was only the one. Loading locally:

gset = getGEO(filename="GSE2034_series_matrix.txt.gz")

However, progressing through the Geo2R code failed soon after:

fvarLabels(gset) <- make.names(fvarLabels(gset))
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘fvarLabels’ for signature ‘"factor"’

 

I've been able to perform some very limited troubleshooting, however, I would really appreciate understanding from someone with a lot more experience than myself. I am convinced that I am missing something very simply which should make all of the Geo2R code executable straight from the website. 

I should add, I am not behind an institution firewall, simply working from home today. 

Thanks

Anthony 

geoquery geoquery error message • 906 views
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Entering edit mode
@sean-davis-490
Last seen 18 days ago
United States

Please upgrade to the most recent R (at least version 3.4) and Bioconductor (https://www.bioconductor.org/install/). This error has been addressed in more recent versions of GEOquery.

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