[BioC] CDF file

[Michal Okoniewski]

Hello Jay and Celine, 

CDFs for exon arrays are "unsupported" and a bit messy indeed. 
They include control and background probesets that are represented as MM
or single-probe-probesets. 
This makes raw CDFs not useful for BioConductor, and probably that's why
they are not included in the BioC metadata packages. 

The package versions of CDFs with BKG and control probesets removed you
can find at:
http://xmap.picr.man.ac.uk/cdf

There are some other attempts to solve the issue, it is currently
discussed also on affy-aroma list. 

Cheers,
Michal 
  

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Celine
Carret
Sent: 06 December 2007 14:03
To: Jay an; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] CDF file

Hi, by googling the array name, I found this:

http://inn.weizmann.ac.il/bioconductor/packages/1.9/data/annotation/html
/hsex10stv2hsug.html

Isn't it your answer?
Best wishes
Celine

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jay an
Sent: 06 December 2007 13:04
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] CDF file

  hello there,
   
  R could not find huex10stv2cdf and huex10stv2probe in bioconductor
repository.
  where can I get the two files?
   
  Thanks
  Jay
  here is the error message:
  > normalized<-justGCRMA()
  Computing affinities[1] "Checking to see if your internet connection
works..."
  [1] "Environment huex10stv2cdf was not found in the Bioconductor
repository."
  [1] "Checking to see if your internet connection works..."
  [1] "Environment huex10stv2probe was not found in the Bioconductor
repository."
  Error in get(probepackagename) : variable "huex10stv2probe" was not
found
   
  > sessionInfo()
  R version 2.6.0 (2007-10-03)
  i386-pc-mingw32
  locale:
 
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
  attached base packages:
  [1] splines tools stats graphics grDevices utils datasets methods base

  other attached packages:
  [1] gcrma_2.10.0 matchprobes_1.10.0 affy_1.16.0 preprocessCore_1.0.0
  [5] affyio_1.6.1 Biobase_1.16.1
  > 

       
---------------------------------

	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor


--
 The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor

--------------------------------------------------------


This email is confidential and intended solely for the u...{{dropped:13}}