Error in read.table, package("gage")

Parharn · 06-05-2014, 07:41 AM

Hi,
I am trying to establish gage protocol by Weijun Luo. I get the following error when I want to load the demo data:

> filename=system.file("exdata/gse16873.demo", package = "gage")
> demo.data=readExpData(filename, row.names=1)
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
In addition: Warning message:
In file(file, "rt") :
file("") only supports open = "w+" and open = "w+b": using the former

Any help?

/Parham

bigmw · 06-07-2014, 12:35 PM

Parham,
You had an typo in the following line, the data directory should be extdata/ not exdata/
filename=system.file("extdata/gse16873.demo", package = "gage")

It works for me:
> filename=system.file("extdata/gse16873.demo", package = "gage")
> demo.data=readExpData(filename, row.names=1)
> str(demo.data)
'data.frame': 100 obs. of 12 variables:
$ HN_1 : num 6.77 6.34 6.59 6.82 7.36 ...
$ DCIS_1: num 6.46 6.76 6.79 6.59 7.31 ...
$ HN_2 : num 6.92 7.18 6.74 6.51 7.39 ...
$ DCIS_2: num 6.77 6.84 6.77 6.41 7.33 ...
…

Parharn · 06-07-2014, 12:37 PM

Yes bigmw, I figured later. Thanks though.
Are you good at gage? I have another thread asking a problem.

/parham

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06-05-2014, 07:41 AM	#1
Parharn Member Location: Sweden Join Date: Jul 2013 Posts: 84	Error in read.table, package("gage") Hi, I am trying to establish gage protocol by Weijun Luo. I get the following error when I want to load the demo data: > filename=system.file("exdata/gse16873.demo", package = "gage") > demo.data=readExpData(filename, row.names=1) Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input In addition: Warning message: In file(file, "rt") : file("") only supports open = "w+" and open = "w+b": using the former Any help? /Parham

06-07-2014, 12:35 PM	#2
bigmw Senior Member Location: US Join Date: Aug 2013 Posts: 123	Parham, You had an typo in the following line, the data directory should be extdata/ not exdata/ filename=system.file("extdata/gse16873.demo", package = "gage") It works for me: > filename=system.file("extdata/gse16873.demo", package = "gage") > demo.data=readExpData(filename, row.names=1) > str(demo.data) 'data.frame': 100 obs. of 12 variables: $ HN_1 : num 6.77 6.34 6.59 6.82 7.36 ... $ DCIS_1: num 6.46 6.76 6.79 6.59 7.31 ... $ HN_2 : num 6.92 7.18 6.74 6.51 7.39 ... $ DCIS_2: num 6.77 6.84 6.77 6.41 7.33 ... …

06-07-2014, 12:37 PM	#3
Parharn Member Location: Sweden Join Date: Jul 2013 Posts: 84	Yes bigmw, I figured later. Thanks though. Are you good at gage? I have another thread asking a problem. /parham