affy snp wrote:
>
> Hi Ted,
>
> My matrix looks like:
>
>> dim(CGH)
> [1] 238304 243
>> CGH[1:30,1:4]
> WM806SignalA WM1716SignalA WM1862SignalA WM1963SignalA
> SNP_A-1909444 1.59 1.48 1.78 2.59
> SNP_A-2237149 2.24 1.87 1.95 2.04
> SNP_A-4303947 2.02 1.70 1.90 2.36
> SNP_A-2236359 2.58 2.06 1.87 2.15
> SNP_A-2205441 1.87 1.46 1.86 2.40
>
>
As others have commented, the problem seems to be with CGH
and not with log2(). str(CGH) should give you more information
about what R thinks CGH is.
Did you forget to set header=TRUE when reading the data in?
Ben Bolker
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