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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"))
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"))
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