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

[Benilton Carvalho]

Thank you all for the report,

I'm going to check what happened and will get back to you ASAP.

b

On Jun 5, 2007, at 11:02 AM, Beth Wilmot wrote:

> 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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>
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