[BioC] cannot open file './', reason 'Permission denied' in: file(file, "r")

[Wolfgang Huber]

Mete,

what is the complete set of 111 values of TargetInfo at maInfo$Filename?

  Best wishes
	Wolfgang

mete at seas.upenn.edu ha scritto:
> 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
>>>
> 
> 


-- 

Best wishes
   Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber