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

[De Bondt, An-7114 [PRDBE]]

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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