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

[mete at seas.upenn.edu]

Hi Wolfgang,

Here is the answer:

> target.info at maInfo$Filename
NULL

Thanks so much for your help.

Mete

Quoting Wolfgang Huber <huber at ebi.ac.uk>:

>
> 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