[BioC] cannot open file './', reason 'Permission denied' in: file(file, "r")
mete at seas.upenn.edu
mete at seas.upenn.edu
Mon Aug 13 01:53:31 CEST 2007
Hi Wolfgang,
Thanks for your quick reply. To answer your questions. TargetInfo is
> TargetInfo
An object of class "marrayInfo"
@maLabels
[1] "AbA1NEW.txt" "AbA2NEW.txt" "AbA3NEW.txt" "AbA4NEW.txt" "AbA5NEW.txt"
111 more elements ...
@maInfo
FileName SampleID HybridizationSeq Cy3 Cy5 HybDate
1 AbA1NEW.txt 113 61 RefRNA AbA1 9/28/2006
2 AbA2NEW.txt 114 77 RefRNA AbA2 10/6/2006
3 AbA3NEW.txt 115 59 RefRNA AbA3 9/29/2006
4 AbA4NEW.txt 116 57 RefRNA AbA4 9/28/2006
5 AbA5NEW.txt 117 55 RefRNA AbA5 9/23/2006
111 more rows ...
@maNotes
[1] "TargetMSS.txt"
and sessionInfo is:
> sessionInfo()
R version 2.5.1 (2007-06-27)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] "grid" "tools" "tcltk" "stats" "graphics" "grDevices"
[7] "utils" "datasets" "methods" "base"
other attached packages:
arrayQuality RColorBrewer gridBase hexbin lattice convert
"1.12.0" "1.0-1" "0.4-3" "1.10.0" "0.16-2" "1.10.0"
marray tkWidgets DynDoc Biobase widgetTools limma
"1.14.0" "1.14.0" "1.14.0" "1.14.1" "1.12.0" "2.9.17"
Quoting Wolfgang Huber <huber at ebi.ac.uk>:
> Dear Mete,
>
> what is the value of your Variable "TargetInfo"? Does it contain empty
> strings? Also, what is the output of sessionInfo()?
>
> Best wishes
> Wolfgang
>
> @seas.upenn.edu ha scritto:
>> Dear All,
>>
>> I get an error message after executing the following commands on RGUI
>>
>>> library(arrayQuality)
>>> library(marray)
>>> TargetInfo<-read.marrayInfo("TargetMSS.txt")
>>> mraw<-read.Agilent(targets=TargetInfo)
>>
>>
>> I get the following:
>>
>> Reading ... ./RCP6NEW.txt
>> Reading ... ./RCP7NEW.txt
>> Reading ... ./RCP8NEW.txt
>> Reading ... ./
>> Error in file(file, "r") : unable to open connection
>> In addition: Warning message:
>> cannot open file './', reason 'Permission denied' in: file(file, "r")
>>
>> The working directory is correct and I do have an active internet
>> connection. I am not sure why I am getting this warning message.
>> Any comments will be appreciated.
>>
>> Best,
>>
>> Mete Civelek
>>
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