[R] problem with normalize.quantiles

[Martin Morgan]

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 <glchen at 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
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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