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

De Bondt, An-7114 [PRDBE] ADBONDT at PRDBE.jnj.com
Mon Jun 4 14:07:35 CEST 2007

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  
> "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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