[BioC] pmStrand() in oligo (version...)
De Bondt, An-7114 [PRDBE]
ADBONDT at PRDBE.jnj.com
Tue Jun 5 08:22:44 CEST 2007
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 ''
3: readChar(con, 5)
2: load(system.file("extdata", paste(annot, "Ref.rda", sep = ""),
package = annot))
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...)
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
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!
> -----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
> If you use the following version instead (which should appear soon on
> BioC), these problems should be taken care of:
> Thank you,
> 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
>> although ?pmStrand is recognised and gives...
>> Returns the strand information on SNP arrays for PM probes (0 -
>> sense / 1 - antisense).
>> object: 'AffySNPPDInfo' object
>> Thanks in advance for your help!
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