[BioC] Problem "Error: is.character(filenames) is not TRUE" in read.xysfiles (Oligo package)

Tommaso Raffaello tommaso.raffaello at helsinki.fi
Wed Apr 23 12:50:50 CEST 2014


Hi,

thanks I solved the problem. The .xys file header was missing. I copied 
it from the .pair files.

Thanks!

Tommaso

On 15/04/2014 17:33, James W. MacDonald wrote:
> Hi Tommaso,
>
> On 4/15/2014 7:03 AM, Tommaso Raffaello wrote:
>> Hi,
>>
>> Thanks! However, I still have some problems.
>>
>> Please see below what I have done. Actually I have downloaded and 
>> installed the "maqcExpression4plex-package" to check the xys files 
>> examples and mine should be ok.
>>
>> What could the problem be?
>>
>> Thank you so much for your help!
>>
>> Tommaso
>>
>> >pine_samples<-read.xysfiles(filenames=xys, 
>> pkgname="pd.110224.pinus.fa.exp.modified", checkType=FALSE)
>> Platform design info loaded.
>> Checking designs for each XYS file...
>> Error in smartReadXYS(filenames, sampleNames) :
>>    Can't find 'designname=' field. C:\HY-data\TORAFFAE\Microarray 
>> Pine experiments\Drained peat Pine 
>> array\Drained_pine_analysis_files/Drained_control_1.xys corrupted?
>
> This error could indicate one of two things. First, the obvious that 
> the file is corrupted. This is probably less likely, and it is more 
> likely that R can't actually find the file itself. Try replacing the 
> backslashes with either doubled backslashes (e.g., 
> C:\\HY-data\\TORAFFAE...) or forward slashes (e.g., 
> C:/HY-data/TORAFFAE...)
>
> Best,
>
> Jim
>
>
>>
>> >sessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United 
>> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
>> [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets 
>> methods   base
>>
>> other attached packages:
>>   [1] pd.110224.pinus.fa.exp.modified_0.0.1 
>> pdInfoBuilder_1.26.0                  oligo_1.26.6
>>   [4] Biostrings_2.30.1 XVector_0.2.0                         
>> IRanges_1.20.7
>>   [7] oligoClasses_1.24.0 affxparser_1.34.2                     
>> RSQLite_0.11.4
>> [10] DBI_0.2-7 Biobase_2.22.0                        BiocGenerics_0.8.0
>>
>> loaded via a namespace (and not attached):
>>   [1] affyio_1.30.0         BiocInstaller_1.12.0 
>> bit_1.1-12            codetools_0.2-8       ff_2.2-13
>>   [6] foreach_1.4.2         GenomicRanges_1.14.4 
>> iterators_1.0.7       preprocessCore_1.24.0 splines_3.0.2
>> [11] stats4_3.0.2          tools_3.0.2           zlibbioc_1.8.0
>> On 12/04/2014 02:49, James W. MacDonald wrote:
>>>
>>> Hi Tommaso,
>>>
>>> If you look at the arguments for read.xysfiles, the first argument 
>>> is '...', in which case you can't do positional argument matching. 
>>> In other words, you need to specify all arguments.
>>>
>>> Read.xysfiles(filenames=xys, <other args>).
>>>
>>> Best,
>>>
>>> Jim
>>>
>>> On Apr 11, 2014 2:24 AM, "Tommaso Raffaello" 
>>> <tommaso.raffaello at helsinki.fi 
>>> <mailto:tommaso.raffaello at helsinki.fi>> wrote:
>>>
>>>     Hi,
>>>
>>>     I have problem in reading my .xys files using the function
>>>     read.xysfiles
>>>     in Oligo package (I have created my .xys based on my .pair files
>>>     following instruction I found on [BioC]).
>>>
>>>     Here is what I have done:
>>>
>>>     >basename(xys)
>>>       [1] "Drained_control_1.xys" "Drained_control_2.xys"            
>>> "Drained_control_3.xys"
>>>       [4] "Drained_infected_resist_1.xys"
>>>     "Drained_infected_resist_2.xys" "Drained_infected_resist_3.xys"
>>>       [7] "Drained_infected_suscep_1.xys"
>>>     "Drained_infected_suscep_2.xys" "Drained_infected_suscep_3.xys"
>>>     [10] "Drained_wounding_1.xys" "Drained_wounding_2.xys"           
>>> "Drained_wounding_3.xys"
>>>     >is.character(xys)
>>>     [1] TRUE
>>>     >read.xysfiles(xys, pd.110224.pinus.fa.exp.modified)
>>>     Error: is.character(filenames) is not TRUE
>>>
>>>     >sessionInfo()
>>>     R version 3.0.2 (2013-09-25)
>>>     Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>
>>>     locale:
>>>     [1] LC_COLLATE=English_United Kingdom.1252
>>>      LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United
>>>     Kingdom.1252
>>>     [4] LC_NUMERIC=C  LC_TIME=English_United Kingdom.1252
>>>
>>>     attached base packages:
>>>     [1] parallel  stats     graphics  grDevices utils datasets
>>>      methods   base
>>>
>>>     other attached packages:
>>>       [1] pd.110224.pinus.fa.exp.modified_0.0.1 pdInfoBuilder_1.26.0
>>>                      oligo_1.26.2
>>>       [4] Biostrings_2.30.1 XVector_0.2.0                          
>>> IRanges_1.20.6
>>>       [7] oligoClasses_1.24.0 affxparser_1.34.2                    
>>>     RSQLite_0.11.4
>>>     [10] DBI_0.2-7 Biobase_2.22.0                         
>>> BiocGenerics_0.8.0
>>>
>>>     loaded via a namespace (and not attached):
>>>       [1] affyio_1.30.0         BiocInstaller_1.12.0 bit_1.1-11    
>>>            codetools_0.2-8       ff_2.2-12
>>>       [6] foreach_1.4.1         GenomicRanges_1.14.4 iterators_1.0.6
>>>           preprocessCore_1.24.0 splines_3.0.2
>>>     [11] stats4_3.0.2          tools_3.0.2 zlibbioc_1.8.0
>>>
>>>
>>>
>>>     (I have previously created the annotation package
>>>     "pd.110224.pinus.fa.exp.modified"with pdInfoBuilder using
>>>     "Drained_control_1.xys" as template with apparently no problems 
>>> and I
>>>     have installed it).
>>>
>>>     Sorry if this is a stupid problem, I´m learning R and 
>>> Bioconductor at
>>>     the same time in these weeks but I couldn´t find info about this
>>>     problem.
>>>
>>>     Thanks for your help!
>>>
>>>     Tommaso
>>>
>>>     --
>>>     Tommaso Raffaello, PhD
>>>
>>>     University of Helsinki
>>>     Department of Forest Sciences
>>>     Latokartanonkaari 7 PO Box 27
>>>     00014 Helsinki (Finland)
>>>
>>>     Phone number: +358 504486086
>>>     email: tommaso.raffaello at helsinki.fi
>>>     <mailto:tommaso.raffaello at helsinki.fi>
>>>     email: tommaso.raffaello at gmail.com
>>>     <mailto:tommaso.raffaello at gmail.com>
>>>
>>>
>>>             [[alternative HTML version deleted]]
>>>
>>>
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>>>
>>
>> -- 
>> Tommaso Raffaello, PhD
>>
>> University of Helsinki
>> Department of Forest Sciences
>> Latokartanonkaari 7 PO Box 27
>> 00014 Helsinki (Finland)
>>
>> Phone number: +358 504486086
>> email:tommaso.raffaello at helsinki.fi
>> email:tommaso.raffaello at gmail.com
>

-- 
Tommaso Raffaello, PhD

University of Helsinki
Department of Forest Sciences
Latokartanonkaari 7 PO Box 27
00014 Helsinki (Finland)

Phone number: +358 504486086
email: tommaso.raffaello at helsinki.fi
email: tommaso.raffaello at gmail.com



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