[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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