[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
On 4/15/2014 7:03 AM, Tommaso Raffaello wrote:
> 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!
> >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...)
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>  LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
>  LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
> attached base packages:
>  parallel stats graphics grDevices utils datasets methods base
> other attached packages:
>  pd.110224.pinus.fa.exp.modified_0.0.1 pdInfoBuilder_1.26.0 oligo_1.26.6
>  Biostrings_2.30.1 XVector_0.2.0 IRanges_1.20.7
>  oligoClasses_1.24.0 affxparser_1.34.2 RSQLite_0.11.4
>  DBI_0.2-7 Biobase_2.22.0 BiocGenerics_0.8.0
> loaded via a namespace (and not attached):
>  affyio_1.30.0 BiocInstaller_1.12.0 bit_1.1-12 codetools_0.2-8 ff_2.2-13
>  foreach_1.4.2 GenomicRanges_1.14.4 iterators_1.0.7 preprocessCore_1.24.0 splines_3.0.2
>  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>).
>> On Apr 11, 2014 2:24 AM, "Tommaso Raffaello"
>> <tommaso.raffaello at helsinki.fi
>> <mailto:tommaso.raffaello at helsinki.fi>> wrote:
>> I have problem in reading my .xys files using the function
>> 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:
>>  "Drained_control_1.xys" "Drained_control_2.xys"
>>  "Drained_infected_resist_1.xys"
>> "Drained_infected_resist_2.xys" "Drained_infected_resist_3.xys"
>>  "Drained_infected_suscep_1.xys"
>> "Drained_infected_suscep_2.xys" "Drained_infected_suscep_3.xys"
>>  "Drained_wounding_1.xys" "Drained_wounding_2.xys"
>>  TRUE
>> >read.xysfiles(xys, pd.110224.pinus.fa.exp.modified)
>> Error: is.character(filenames) is not TRUE
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>  LC_COLLATE=English_United Kingdom.1252
>> LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United
>>  LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
>> attached base packages:
>>  parallel stats graphics grDevices utils datasets
>> methods base
>> other attached packages:
>>  pd.110224.pinus.fa.exp.modified_0.0.1 pdInfoBuilder_1.26.0
>>  Biostrings_2.30.1 XVector_0.2.0
>>  oligoClasses_1.24.0 affxparser_1.34.2
>>  DBI_0.2-7 Biobase_2.22.0
>> loaded via a namespace (and not attached):
>>  affyio_1.30.0 BiocInstaller_1.12.0 bit_1.1-11
>> codetools_0.2-8 ff_2.2-12
>>  foreach_1.4.1 GenomicRanges_1.14.4 iterators_1.0.6
>> preprocessCore_1.24.0 splines_3.0.2
>>  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
>> Thanks for your help!
>> 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>
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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.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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