Hi Henrik,


	Thanks a lot for this excellent suggestion. Especially the sample code
would help. I would try to use binary in version 11 of custom CDF.

Best,
Manhong
On Tue, 2008-05-27 at 07:43 -0700, Henrik Bengtsson wrote:
> Hi Manhong,
> 
> thanks for doing this big job.  In you previous releases you have
> generated ASCII CDF files.  Thinking beyond R, would you mind
> releasing binary CDF files instead?  They are much faster and memory
> efficient to read (e.g. using Affymetrix Fusion SDK via R package
> affxparser)?  A binary CDF is also much smaller (25-50% of the size).
> Given an ASCII CDF, it is easy to convert it to binary (v4/XDA) using
> convertCdf() in affxparser, e.g.
> 
> > library(affxparser)
> > convertCdf("ASCII/AtGenome_At_REFSEQ.cdf", "AtGenome_At_REFSEQ.cdf")
> > hdr <- readCdfHeader("AtGenome_At_REFSEQ.cdf")
> > str(hdr)
> List of 12
>  $ ncols      : int 534
>  $ nrows      : int 534
>  $ nunits     : int 8990
>  $ nqcunits   : int 13
>  $ refseq     : chr ""
>  $ chiptype   : chr "AtGenome_At_REFSEQ"
>  $ filename   : chr "./AtGenome_At_REFSEQ.cdf"
>  $ rows       : int 534
>  $ cols       : int 534
>  $ probesets  : int 8990
>  $ qcprobesets: int 13
>  $ reference  : chr ""
> 
> > file.info("ASCII/AtGenome_At_REFSEQ.cdf")$size
> [1] 23214131
> > file.info("AtGenome_At_REFSEQ.cdf")$size
> [1] 5632960
> 
> Cheers
> 
> Henrik
> 
> On Tue, May 27, 2008 at 6:36 AM, Manhong Dai <daimh@umich.edu> wrote:
> > Hi Burak,
> >
> >
> >        Thanks a lot for your interest in our custom CDF.
> >
> >
> >        I am working hard on version 11, because this time we planed to support
> > almost all Affymetrix chips and some kinds of one-mismatch probe
> > sequence alignment. The data I am processing is at Tera-byte level.
> >
> >
> >        I expect they would be ready in a couple of weeks. If you would like to
> > sign-up at http://arrayanalysis.mbni.med.umich.edu/ or yahoo mail list
> > customcdf, you will get notification as soon as we release them.
> >
> >
> > Best,
> > Manhong
> >
> > MBNI
> > University of Michigan
> >
> >>Hi
> >>In the current BioC release (2.2), the custom CDF packages are no
> >>longer hosted. I was wondering whether this will be the case in the
> >>following releases or can we expect to see these packages again?
> >>Thanks
> >>-burak
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >

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