[BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")

[James W. MacDonald]

Hi Simone,

On 5/29/2012 9:18 AM, Simone [guest] wrote:
> Hi!
>
> Currently I am trying to use the library "GEOquery" to retrieve meta information (phenodata information) and the data tables of GEO samples (from GEO series without GEO datasets).
>
> I already have got the data (.soft.gz files), so I tried it the following way for example:
>
> GSE19711<- getGEO(filename=system.file("mypath/GSE19711_family.soft.gz", package="GEOquery"))

Why are you using system.file() in this context? Did you really download 
the soft file to your GEOquery library directory? That seems odd to me.

The default is to download to a tempdir, which is likely to be something 
like

C:\Users\<yourusername>\AppData\Local\Temp\<sometmpdir>

or did you download somewhere else? Where does mypath point?

Best,

Jim




>
> But I get the following error:
>
> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>    invalid 'nlines' argument
> In addition: Warning messages:
> 1: In file(fname, "r") :
>    file("") only supports open = "w+" and open = "w+b": using the former
> 2: In file(con, "r") :
>    file("") only supports open = "w+" and open = "w+b": using the former
> 3: In file(fname, "r") :
>    file("") only supports open = "w+" and open = "w+b": using the former
>
> I tried it on windows and linux and also with the newest version of R and GEOquery.
>
> On both machines there occurs the same error, also with other GEO accession numbers.
>
> What is going wrong and what can I do to get the information I need?
>
> When I use a path to my file which is not existing, I get the same error, but I am quite sure that I set the working directory and path to the GEO file correctly.
>
> Greets,
> Simone
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=German_Austria.1252  LC_CTYPE=German_Austria.1252    LC_MONETARY=German_Austria.1252
> [4] LC_NUMERIC=C                    LC_TIME=German_Austria.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.23.3     Biobase_2.16.0      BiocGenerics_0.2.0  BiocInstaller_1.4.4
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1.1 tools_2.15.0   XML_3.9-4.1
>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8
>   [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.21.9 Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1 tools_2.14.1 XML_3.9-4
>
>> traceback()
> 6: read.table(con, sep = "\t", header = FALSE, nrows = nseries)
> 5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
> 4: suppressWarnings(read.table(con, sep = "\t", header = FALSE,
>         nrows = nseries))
> 3: parseGSEMatrix(fname)
> 2: parseGEO(filename, GSElimits)
> 1: getGEO(filename = system.file("homo_sapiens/peripheral_whole_blood/GSE19711/GSE19711_family.soft.gz",
>         package = "GEOquery"))
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099