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Question: R matrix size limits and array data
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gravatar for Rob Dunne
5.1 years ago by
Rob Dunne230
Rob Dunne230 wrote:
Hi, I am hitting the 2^31-1 limit on array entries in loading and normalizing a set of exon arrays. The oligo package uses "ff" if you have it loaded but ff seems to have the same limit. I have modified some routines from an older version of oligo (1.10.4) to use big.matrix from the big.memory package. This necessitated making big.matrix methods for is.matrix, annotatedDataFrameFrom, and possibly some other things. It works but is probably very fragile. How are other people handling the 2^(31)-1 limit on matrix sizes? R
ADD COMMENTlink modified 5.1 years ago by Benilton Carvalho4.2k • written 5.1 years ago by Rob Dunne230
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gravatar for Benilton Carvalho
5.1 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.2k wrote:
You can always use NetCDF and HDF5. Even with ff, you can combine different virtual data frames to work around that, as what we do in crlmm. b On Friday, 19 October 2012, Rob Dunne wrote: > Hi, > > I am hitting the 2^31-1 limit on array entries in loading and normalizing > a set of exon arrays. The oligo package uses "ff" if you have it loaded > but ff > seems to have the same limit. > > I have modified some routines from an older version of oligo (1.10.4) to > use > big.matrix from the big.memory package. This necessitated making big.matrix > methods for is.matrix, annotatedDataFrameFrom, and possibly some other > things. > It works but is probably very fragile. > > How are other people handling the 2^(31)-1 limit on matrix sizes? > > R > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <javascript:;> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.1 years ago by Benilton Carvalho4.2k
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