again, the bioconductor list is appropriate. You'll want to be sure to update your packages using the instructions at
http://bioconductor.org/docs/install/ and be sure to provide the output of sessionInfo() to make any actual problems easier to track down. Martin George Chen <glc...@stanford.edu> writes: > Hi All, > > I am using normalize.quantiles (package preprocessCore) to process a 8300 row > x 96 col matrix, all numerical data. > > When I limit the input matrix to 8300 x 67, the function works fine and my > data is normalized. But when I increase the input matrix size to 8300 x 68, > the function processes but instead of giving normalized data, it gives me all > the same number. With 96 columns (the whole matrix), much the same happens. > > Has anyone had any experience with this and what to do about it. I would > really like to not have to prune my dataset. > > Examples: > > Limited input matrix (col = 67) > [,1] [,2] [,3] [,4] [,5] > [1,] NA 5977.433 5555.572 6826.831 4142.117 > [2,] 3012.837 6617.005 6036.862 7796.186 5453.295 > [3,] NA 5977.433 7192.046 7582.068 6042.775 > [4,] 1780.039 1732.662 6373.366 7825.302 6775.492 > [5,] NA 3308.601 2297.677 7294.935 1482.699 > [6,] NA 3569.632 3509.979 3566.683 NA > [7,] NA 4492.529 6399.490 4925.750 1921.428 > [8,] NA 2416.358 3958.061 4592.030 2829.436 > [9,] 7889.050 7928.198 7929.257 7930.121 7927.907 > [10,] 7542.413 7893.827 7889.407 7896.078 7894.852 > > 78 col input matrix > [,1] [,2] [,3] [,4] [,5] > [1,] NA 7883.356 7883.356 7883.356 7883.356 > [2,] 7883.356 7883.356 7883.356 7883.356 7883.356 > [3,] NA 7883.356 7883.356 7883.356 7883.356 > [4,] 7883.356 7883.356 7883.356 7883.356 7883.356 > [5,] NA 7883.356 7883.356 7883.356 7883.356 > [6,] NA 7883.356 7883.356 7883.356 NA > [7,] NA 7883.356 7883.356 7883.356 7883.356 > [8,] NA 7883.356 7883.356 7883.356 7883.356 > [9,] 7883.356 7883.356 7883.356 7883.356 7883.356 > [10,] 7883.356 7883.356 7883.356 7883.356 7883.356 > > whole input matrix (96 col) > [,1] [,2] [,3] [,4] [,5] > [1,] NA 7747.377 7747.377 7747.377 7747.377 > [2,] 7747.377 7747.377 7747.377 7747.377 7747.377 > [3,] NA 7747.377 7747.377 7747.377 7747.377 > [4,] 7747.377 7747.377 7747.377 7747.377 7747.377 > [5,] NA 7747.377 7747.377 7747.377 7747.377 > [6,] NA 7747.377 7747.377 7747.377 NA > [7,] NA 7747.377 7747.377 7747.377 7747.377 > [8,] NA 7747.377 7747.377 7747.377 7747.377 > [9,] 7747.377 7747.377 7747.377 7747.377 7747.377 > [10,] 7747.377 7747.377 7747.377 7747.377 7747.377 > > Thanks in advance, > > George > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.