It sounds strange. I would check that it has a traditional PM/MM design. I would also check whether there is several groups in each unit or only one. Anyway, since you have tried doing this before, I would suggest using for example readCdf from affxparser and then construct the cdf environment by hand. That should be somewhat easy, if you have experience with cdf environments. A cdf package is essentially a wrapper around a cdf environment. Kasper On Feb 17, 2009, at 9:26 , Jiang, Zhen wrote: > It's a custom Affy array. Because of company confidentiality, I'm not > sure if I should reveal the name. > The probeset size is only 3. So the number of probesets are huge > comparing to normal Affy arrays, which have probeset size about 9 to > 11. > I have made three CDF packages before. The results almost came > instantly > for those three. > Now this time, it's has been running for more than 3 days and I > haven't > got any output yet. That's why I'm asking if it is normal or it > indicates something is wrong with my code or the file. > > Thanks, > > Zhen Jiang > > > -----Original Message----- > From: Kasper Daniel Hansen [mailto:khansen at stat.berkeley.edu] > Sent: Monday, February 16, 2009 3:24 PM > To: Jiang, Zhen > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Running time for make.cdf.package > > Why don't you tell us the size of the chip, ie. number of probes and > number of probesets. You might even want to reveal the actual name > (!). Since it is human, I guess it is pretty big. Your main problem is > probably memory or a faulty file. In general, making a CDF package is > pretty quick. I would be shocked if it took more than 1 hour on a > suitable computer. > > Do you get any output, since you are running with verbose = TRUE. > > Kasper > > On Feb 16, 2009, at 9:57 , Jiang, Zhen wrote: > >> Dear list, >> >> I have a CDF file of size 404,514KB. I'm using the following code to >> build a package from it. >> >> library(affy) >> library(makecdfenv) >> >> ## CDF Package >> make.cdf.package("xxxx.CDF", >> species="Homo_sapiens", >> version="0.0.1",unlink=TRUE, >> verbose=TRUE) >> >> It has been running for two and half days. Is it because the CDF is >> too >> large for R to handle or something is wrong with my code? >> I have successfully build R packages for other much smaller CDF files >> using the same code, only with different CDF name. >> >> The sessionInfo() is listed below. >> >>> sessionInfo() >> R version 2.7.0 (2008-04-22) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets >> methods >> >> [8] base >> >> other attached packages: >> [1] makecdfenv_1.18.0 affy_1.18.2 preprocessCore_1.2.1 >> [4] affyio_1.8.1 Biobase_2.0.1 >> >> Thank you very much. >> >> Zhen Jiang >> >> >> Notice: This e-mail message, together with any attachme...{{dropped: >> 15}} >> >> _______________________________________________ >> 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 > > Notice: This e-mail message, together with any attach...{{dropped:13}}