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 > > [[alternative HTML version deleted]]