[BioC] How to get the relative path with list.celfiles() from the oligo package?

[Benilton Carvalho]

reinstall it... as a bonus, you'll get a slightly newer version.

source("http://www.bioconductor.org/biocLite.R")
biocLite("oligo")


On Aug 20, 2009, at 9:11 PM, Peng Yu wrote:

> I see. So we have the same version of oligo installed. But my document
> for oligo is less than yours. Can somebody help me on this issue?
>
> Regards,
> Peng
>
> On Thu, Aug 20, 2009 at 6:56 PM, Benilton  
> Carvalho<bcarvalh at jhsph.edu> wrote:
>> Hi Peng,
>>
>> That's not what I meant. My point was that my oligo version is the  
>> same as
>> yours. Therefore, the documentation must be the same. And mine  
>> describes the
>> use of "..." (dots).
>>
>> b
>>
>> On Aug 20, 2009, at 8:43 PM, Peng Yu wrote:
>>
>>> Hi,
>>>
>>> So in summary, you use an older version of R than mine, but you  
>>> get a
>>> newer version of help page. This is really strange. Can somebody  
>>> help
>>> me figure out what the problem is with my R installation?
>>>
>>> Regards,
>>> Peng
>>>
>>> On Thu, Aug 20, 2009 at 4:51 PM, Benilton Carvalho<bcarvalh at jhsph.edu 
>>> >
>>> wrote:
>>>>
>>>> Peng,
>>>>
>>>> the part that was omitted in your message was:
>>>>
>>>> Arguments:
>>>>
>>>>  ...: parameters to be passed to 'list.files'
>>>>
>>>> and note my sessionInfo() (it's a very old R 2.9.x that I'm  
>>>> running, but
>>>> it
>>>> doesn't play a role in this case).
>>>>
>>>> b
>>>>
>>>>> sessionInfo()
>>>>
>>>> R version 2.9.0 RC (2009-04-10 r48321)
>>>> x86_64-unknown-linux-gnu
>>>>
>>>> locale:
>>>>
>>>> LC_CTYPE 
>>>> = 
>>>> en_US 
>>>> .iso885915 
>>>> ;LC_NUMERIC 
>>>> = 
>>>> C 
>>>> ;LC_TIME 
>>>> = 
>>>> en_US 
>>>> .iso885915 
>>>> ;LC_COLLATE 
>>>> = 
>>>> en_US 
>>>> .iso885915 
>>>> ;LC_MONETARY 
>>>> = 
>>>> C 
>>>> ;LC_MESSAGES 
>>>> = 
>>>> en_US 
>>>> .iso885915 
>>>> ;LC_PAPER 
>>>> = 
>>>> en_US 
>>>> .iso885915 
>>>> ;LC_NAME 
>>>> = 
>>>> C 
>>>> ;LC_ADDRESS 
>>>> = 
>>>> C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods    
>>>> base
>>>>
>>>> other attached packages:
>>>> [1] oligo_1.8.1          preprocessCore_1.6.0 oligoClasses_1.6.0
>>>> [4] Biobase_2.4.1
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] affxparser_1.17.2  affyio_1.12.0      Biostrings_2.11.52  
>>>> DBI_0.2-4
>>>> [5] IRanges_1.1.66     splines_2.9.0
>>>>
>>>>
>>>> On Aug 20, 2009, at 6:10 PM, Peng Yu wrote:
>>>>
>>>>> On Thu, Aug 20, 2009 at 3:31 PM, Sean Davis<seandavi at gmail.com>  
>>>>> wrote:
>>>>>>
>>>>>>
>>>>>> On Thu, Aug 20, 2009 at 4:24 PM, Peng Yu <pengyu.ut at gmail.com>  
>>>>>> wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I run the following command. But it only gives the file names.  
>>>>>>> I am
>>>>>>> wondering if there is a way to get the filename along with the
>>>>>>> directory name, i.e., 'data/ki10923.CEL', etc.
>>>>>>>
>>>>>>> Regards,
>>>>>>> Peng
>>>>>>>
>>>>>>>> list.celfiles('data/')
>>>>>>>
>>>>>>> [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL"
>>>>>>> "ki10928.CEL"
>>>>>>> [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL"
>>>>>>> "wt10980.CEL"
>>>>>>
>>>>>> Hi, Peng.
>>>>>>
>>>>>> Reading the help for list.celfiles(), it suggests that all  
>>>>>> arguments
>>>>>> are
>>>>>> passed along to the list.files().  Reading the help for  
>>>>>> list.files()
>>>>>> suggests that including full.names=TRUE will return the  
>>>>>> information you
>>>>>> want.
>>>>>>
>>>>>> Sean
>>>>>>
>>>>>>
>>>>>
>>>>> I have checked the help page before I sent the message. But the  
>>>>> help
>>>>> page that I got did not show much information. See below the  
>>>>> email. My
>>>>> sessionInfo is shown below the help page. Is my documentation
>>>>> outdated? I remember that my R installation was updated only two  
>>>>> weeks
>>>>> ago.
>>>>>
>>>>> Regards,
>>>>> Peng
>>>>>
>>>>> list.celfiles             package:oligo             R  
>>>>> Documentation
>>>>>
>>>>> List CEL/XYS files
>>>>>
>>>>> Description:
>>>>>
>>>>> Lists the CEL/XYS files.
>>>>>
>>>>> Usage:
>>>>>
>>>>> list.celfiles(...)
>>>>>
>>>>> Arguments:
>>>>>
>>>>>
>>>>>
>>>>> Value:
>>>>>
>>>>> Character vector with the filenames.
>>>>>
>>>>> Examples:
>>>>>
>>>>> list.xysfiles()
>>>>> list.celfiles()
>>>>>
>>>>>
>>>>>
>>>>>> sessionInfo()
>>>>>
>>>>> R version 2.9.1 (2009-06-26)
>>>>> x86_64-unknown-linux-gnu
>>>>>
>>>>> locale:
>>>>>
>>>>>
>>>>> LC_CTYPE 
>>>>> = 
>>>>> en_US 
>>>>> .UTF 
>>>>> -8 
>>>>> ;LC_NUMERIC 
>>>>> = 
>>>>> C 
>>>>> ;LC_TIME 
>>>>> = 
>>>>> en_US 
>>>>> .UTF 
>>>>> -8 
>>>>> ;LC_COLLATE 
>>>>> = 
>>>>> en_US 
>>>>> .UTF 
>>>>> -8 
>>>>> ;LC_MONETARY 
>>>>> = 
>>>>> C 
>>>>> ;LC_MESSAGES 
>>>>> = 
>>>>> en_US 
>>>>> .UTF 
>>>>> -8 
>>>>> ;LC_PAPER 
>>>>> = 
>>>>> en_US 
>>>>> .UTF 
>>>>> -8 
>>>>> ;LC_NAME 
>>>>> = 
>>>>> C 
>>>>> ;LC_ADDRESS 
>>>>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>>>>
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  methods    
>>>>> base
>>>>>
>>>>> other attached packages:
>>>>> [1] oligo_1.8.1          preprocessCore_1.6.0 oligoClasses_1.6.0
>>>>> [4] Biobase_2.4.1
>>>>>
>>>>> loaded via a namespace (and not attached):
>>>>> [1] affxparser_1.16.0 affyio_1.12.0     Biostrings_2.12.8  
>>>>> DBI_0.2-4
>>>>> [5] IRanges_1.2.3     splines_2.9.1
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
>>>
>>> _______________________________________________
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>>
>>
>
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