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

James W. MacDonald jmacdon at u.washington.edu
Tue Apr 15 16:33:35 CEST 2014


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

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099



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