I am trying to use GEOquery to download the data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39133. Based on the vignette, I should be able to just run the code:
gse <- getGEO('GSE39133')
This produces the following output:
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39133/matrix/ Found 1 file(s) GSE39133_series_matrix.txt.gz trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39133/matrix/GSE39133_series_matrix.txt.gz' ftp data connection made, file length 14943474 bytes ================================================== downloaded 14.3 MB Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) : cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL570&form=text&view=full'
When I navigate in my web browser to the link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL570&form=text&view=full, I can find it and it starts to download.
I am a bit confused as to what is happening. Because according to the getGEO documentation, it states:
GSEMatrix: A boolean telling GEOquery whether or not to use GSE Series Matrix files from GEO. The parsing of these files can be many orders-of-magnitude faster than parsing the GSE SOFT format files. Defaults to TRUE, meaning that the SOFT format parsing will not occur; set to FALSE if you for some reason need other columns from the GSE records.
So if the SOFT file is not being parsed, why is it downloading it? Perhaps I am missing something here...
Any help would be appreciated. Many thanks in advance,
> sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin11.0.0 (64-bit) Running under: OS X 10.10.5 (Yosemite) locale:  en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  GEOquery_2.38.4 Biobase_2.32.0 BiocGenerics_0.20.0  nvimcom_0.9-14 loaded via a namespace (and not attached):  httr_1.2.0 R6_2.1.2 tools_3.3.1 RCurl_1.95-4.8 bitops_1.0-6