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

[mete at seas.upenn.edu]

Hi Wolfgang,

Thanks for pointing me out to the right direction. After looking at  
TargetInfo at maInfo, I realized that there were three extra lines in the  
TargetMSS.txt file. That is why I was getting an error message.

Thanks again,

Best,

Mete

Quoting 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
>
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