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
