[BioC] Fwd: pmStrand() in oligo (version...)

[Beth Wilmot]

Hello,
I am having the same difficulty with both nsp and sty pkgs.  I
re-installed the pd. mapping pkgs from bioconductor and still have only
the two:

[1] "pd.mapping250k.nsp.sqlite" "seqMat.rda"  

Thanks,
Beth


>>> "Benilton Carvalho" <bcarvalh at jhsph.edu> 6/5/2007 6:23:10 AM >>>


Begin forwarded message:

> From: Benilton Carvalho <bcarvalh at jhsph.edu>
> Date: June 5, 2007 9:22:14 AM EDT
> To: "De Bondt, An-7114 [PRDBE]" <ADBONDT at PRDBE.jnj.com>
> Subject: Re: [BioC] pmStrand() in oligo (version...)
>
> Hi An,
>
> this is not what you're expected to have. My suggestion is to  
> reinstall the pd.mapping pkg.
>
> What you should have is:
>
> [1] "pd.mapping250k.styCrlmmInfo.rda"
> [2] "pd.mapping250k.sty.spline.params.rda"
> [3] "pd.mapping250k.sty.sqlite"
> [4] "seqMat.rda"
>
> b
>
> On Jun 5, 2007, at 2:38 AM, De Bondt, An-7114 [PRDBE] wrote:
>
>> Hi Ben,
>>
>>> dir(system.file("extdata", package = "pd.mapping250k.sty"))
>> [1] "pd.mapping250k.sty.sqlite" "seqMat.rda"
>>
>> Is this the output what it should be?
>>
>> An
>>
>>
>> -----Original Message-----
>> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] 
>> Sent: Tuesday, 5 June 2007 8:34
>> To: De Bondt, An-7114 [PRDBE]
>> Cc: bioconductor at stat.math.ethz.ch 
>> Subject: Re: [BioC] pmStrand() in oligo (version...)
>>
>>
>> That's strange An.
>>
>> Could you please tell us what you get with:
>>
>> dir(system.file("extdata", package = "pd.mapping250k.sty"))
>>
>> I wonder if there was a problem when you installed the pd.mapping
>> package, as it (v. 0.2.5) does contain the Ref file application is
>> complaining about...
>>
>> cheers,
>> b
>>
>>
>> On Jun 5, 2007, at 2:22 AM, De Bondt, An-7114 [PRDBE] wrote:
>>
>>> Hi Ben,
>>>
>>> Here some extra info, hopefully useful to pinpoint the issue:
>>>
>>>> rmaSty <- snprma(fsetSty)
>>>      This may take a while.
>>>      Adjusting for sequence and fragment length....... done.
>>>      Normalizing...Error in readChar(con, 5) : cannot open the
>>> connection
>>>      In addition: Warning message:
>>>      cannot open compressed file ''
>>>> traceback()
>>>      3: readChar(con, 5)
>>>      2: load(system.file("extdata", paste(annot, "Ref.rda", sep = 

>>> ""),
>>>        package = annot))
>>>      1: snprma(fsetSty)
>>>> package.version("pd.mapping250k.sty")
>>>      [1] "0.2.5"
>>>
>>>
>>> Cheers,
>>> An
>>>
>>>
>>> -----Original Message-----
>>> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] 
>>> Sent: Monday, 4 June 2007 17:02
>>> To: De Bondt, An-7114 [PRDBE]
>>> Cc: bioconductor at stat.math.ethz.ch 
>>> Subject: Re: [BioC] pmStrand() in oligo (version...)
>>>
>>>
>>> Hi An,
>>>
>>> that's problably R complaining a file that it didn't find. The
>>> strange thing is that I can't reproduce it here. Could you please
>>> forward me the results of traceback()?
>>>
>>> This would happen if, for example, oligo finds the old version of 

>>> the
>>> pd.mapping250k.sty package.
>>>
>>> b
>>>
>>> On Jun 4, 2007, at 8:07 AM, De Bondt, An-7114 [PRDBE] wrote:
>>>
>>>> Hi Ben,
>>>>
>>>> When using oligo version 1.0.2-3, the pmStrand function indeed
>>>> works :-)
>>>> but the snprma function results in an error:
>>>>
>>>>      fsetSty <- read.celfiles(dir()[grep("S.CEL", dir())])
>>>>      rmaSty <- snprma(fsetSty)
>>>>
>>>> Normalizing...Error in readChar(con, 5) : cannot open the  
>>>> connection
>>>> In addition: Warning message:
>>>> cannot open compressed file
>>>>
>>>> How can I check which connection needs to be established?
>>>>
>>>> Thanks in advance for your help!
>>>> An
>>>>
>>>> -----Original Message-----
>>>> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] 
>>>> Sent: Friday, 1 June 2007 15:30
>>>> To: De Bondt, An-7114 [PRDBE]
>>>> Cc: bioconductor at stat.math.ethz.ch 
>>>> Subject: Re: [BioC] pmStrand() in oligo (version...)
>>>>
>>>>
>>>> Hi An,
>>>>
>>>> I fixed that problem, thanks for the report.
>>>>
>>>> Also, regarding the .crlmm.regions packages, these are not
anymore
>>>> required.
>>>>
>>>> If you use the following version instead (which should appear  
>>>> soon on
>>>> BioC), these problems should be taken care of:
>>>>
>>>> http://www.biostat.jhsph.edu/~bcarvalh/oligo_1.0.2-3.tar.gz 
>>>>
>>>> Thank you,
>>>>
>>>> b
>>>>
>>>> On Jun 1, 2007, at 5:10 AM, De Bondt, An-7114 [PRDBE] wrote:
>>>>
>>>>> Dear useRs,
>>>>>
>>>>> I am looking into the raw data of the 500K SNP arrays and I
would
>>>>> like to
>>>>> select the data from only one strand, sense OR antisense.  How
>>>>> could I do
>>>>> this?  Probably something like:
>>>>>
>>>>>      fsetSty <- read.celfiles(dir()[grep("S.CEL", dir())])
>>>>>      strand.sty <- pmStrand(get(annotation(fsetSty)))
>>>>>
>>>>> but the last command results in "Error: could not find function
>>>>> "pmStrand""
>>>>> although ?pmStrand is recognised and gives...
>>>>>
>>>>> Description:
>>>>>      Returns the strand information on SNP arrays for PM probes 

>>>>> (0 -
>>>>>      sense / 1 - antisense).
>>>>> Usage:
>>>>>      pmStrand(object)
>>>>> Arguments:
>>>>>   object: 'AffySNPPDInfo' object
>>>>>
>>>>>
>>>>>
>>>>> Thanks in advance for your help!
>>>>> An
>>>>>
>>>>>
>>>>> 	[[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
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>>>>> gmane.science.biology.informatics.conductor
>

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