I tried recently somme tutorial on microarray data analysis, using either the following link: http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/ or the chapter on bioconductor from "R in a nutshell". After installing and loading the GEOquery package, I tried loading data as indicated:
and I was returned the following error message, in both cases:
 "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE20986/" Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 6 elements
This is only an example, since the file involved in "R in a nutshell" is GSE2034, producing the same error. As I understand the error message, it tells me that the line 1 has a size different from the 6 elements expected for the data.frame; this is supprising for data retrieved from the NCBI server; so I think something else is faulty. Did anyone has had such an error and found what was wrong and how bypass this block. Thanks in advance.
I use R 2.15.1 on ubuntu 12.04, with bioconductor 2.10; here is the result of sessionInfo():
R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale:  LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C  LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8  LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  GEOquery_2.23.5 Biobase_2.16.0 BiocGenerics_0.2.0  BiocInstaller_1.4.7 loaded via a namespace (and not attached):  RCurl_1.91-1 tools_2.15.1 XML_3.9-4