[R] How to log-2 transform a matrix

[affy snp]

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

Even I tried log2(CGH[1:238304,1:243]), it did not work either. Based
on the error
message, which is:

> CGHlog2<-log2(CGH[1:238304,1:243])
Error in Math.data.frame(CGH[1:238304, 1:243]) :
  non-numeric variable in data frame:
WM806SignalAWM1716SignalAWM1862SignalAWM1963SignalAWM1968SignalAWM1976SignalAWM3228SignalAWM3457SignalAWM3061SignalAWM3246SignalAWM3282SignalAWM1931SignalAWM1026SignalAWM3670SignalAWM3702SignalAWM3482SignalAWM3311SignalAWM1960SignalAWM1720SignalAWM3215SignalAWM3451SignalAWM3130SignalAWM2029SignalAWM3243NCI.A5SignalAWM1745SignalAWM3526SignalAWM3682SignalAWM3623SignalAWM3450SignalAWM853.2SignalAWM1930SignalAWM3244NCI.BSignalAWM984SignalAWM3619SignalAWM3297SignalAWM451LuSignalAWM3077SignalAWM3381ASignalAWM3627SignalAWM3218SignalAWM3163SignalAWM3259SignalAWM3506SignalAWM3629SignalAWM3456SignalAWM1346SignalAWM1852SignalARCC13NSignalAJAPOV46NSignalAJAPOV75NSignalAS004285NSignalARCC50NSignalAJAPOV54NSignalAJAPOV92NSignalARCC56NSignalAS004288NSignalAS004295NSignalAS004292NSignalAJAPOV73NSignalAJAPOV52NSignalARCC53NSignalAS004289NSignalARCC25NSignalAS004294NSignalAS004275NSignalAJAPOV32NSignalACN37SignalACN16SignalAS004291NSignalACN17SignalARCC129NS

it seems that the column names was messed up. How to solve this?

Thanks!

Allen

On Nov 10, 2007 9:43 AM, Ted Harding <Ted.Harding at manchester.ac.uk> wrote:
> On 10-Nov-07 14:25:32, affy snp wrote:
> > Dear list,
> > I am wondering how to log-2 based transform a matrix
> > with numeric values?
> > I tried > CGHlog2<-log2(CGH) but got an error. Then I
> > found for log2(x) in R, the x has to be a numeric or
> > complex vector. Any method for a matrix?
>
> Yes, simply the method you tried: log2(M) where M is
> the matrix of numeric/complex datavalues.
>
> log2() will work just as well on a dataframe whose
> contents are numerical, as on a simple matrix:
>
> M<-data.frame(A=c(1,2,3,4),B=c(2,3,4,5),C=c(3,4,5,6))
> log2(M)
>          A        B        C
> 1 0.000000 1.000000 1.584963
> 2 1.000000 1.584963 2.000000
> 3 1.584963 2.000000 2.321928
> 4 2.000000 2.321928 2.584963
>
> From the error message you quote below, it looks as
> though you have made a mess of reading in, or constructing,
> the dataframe (the output looks like a series of several
> variables names, all concatenated together into one long
> string value).
>
> Hoping this helps!
> Ted.
>
> > Thanks a lot and have a good weekend!
> >
> > Allen
> >
> >
> >>Error in Math.data.frame(CGH) :
> >   non-numeric variable in data frame:
> > WM806SignalAWM1716SignalAWM1862SignalAWM1963SignalAWM1968SignalAWM1976Si
> > gnalAWM3228SignalAWM3457SignalAWM3061SignalAWM3246SignalAWM3282SignalAWM
> > 1931SignalAWM1026SignalAWM3670SignalAWM3702SignalAWM3482SignalAWM3311Sig
> > nalAWM1960SignalAWM1720SignalAWM3215SignalAWM3451SignalAWM3130SignalAWM2
> > 029SignalAWM3243NCI.A5SignalAWM1745SignalAWM3526SignalAWM3682SignalAWM36
> > 23SignalAWM3450SignalAWM853.2SignalAWM1930SignalAWM3244NCI.BSignalAWM984
> > SignalAWM3619SignalAWM3297SignalAWM451LuSignalAWM3077SignalAWM3381ASigna
> > lAWM3627S
> > ignalAWM3218SignalAWM3163SignalAWM3259SignalAWM3506SignalAWM3629SignalAW
> > M3456SignalAWM1346SignalAWM1852SignalARCC13NSignalAJAPOV46NSignalAJAPOV7
> > 5NSignalAS004285NSignalARCC50NSignalAJAPOV54NSignalAJAPOV92NSignalARCC56
> > NSignalAS004288NSignalAS004295NSignalAS004292NSignalAJAPOV73NSignalAJAPO
> > V52NSignalARCC53NSignalAS004289NSignalARCC25NSignalAS004294NSignalAS0042
> > 75NSignalAJAPOV32NSignalACN37SignalACN16SignalAS004291NSignalACN17Signal
> > ARCC129NS
> >
> > ______________________________________________
> > R-help at 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.
>
> --------------------------------------------------------------------
> E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
> Fax-to-email: +44 (0)870 094 0861
> Date: 10-Nov-07                                       Time: 14:43:42
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