[BioC] factDesign - another question

[Denise Scholtens]

Hi again,

The current version of factDesign (1.1.3) does contain log2 transformed
values.  I get the following -

> library(factDesign)
Loading required package: affy
Welcome to Bioconductor
         Vignettes contain introductory material.  To view,
         simply type: openVignette()
         For details on reading vignettes, see
         the openVignette help page.

Synching your local package management information ...
> data(estrogen)
> exprs(estrogen)[1:5,]
             et1.CEL   et2.CEL  Et1.CEL   Et2.CEL  eT1.CEL  eT2.CEL
ET1.CEL
33598_r_at  4.970288  4.652992 4.450018  4.718027 4.760855 4.883518
4.697013
39859_r_at  9.145143  9.055006 9.189090  9.169929 9.328266 9.470384
9.250283
35114_at    7.232742  7.116724 7.345879  7.254973 7.359185 7.545388
7.302415
41041_s_at  6.538163  6.646323 6.608893  6.510601 7.503181 8.143311
7.173642
41759_at   10.286364 10.116122 9.999341 10.043443 9.846629 9.478198
9.813761
            ET2.CEL
33598_r_at 4.568902
39859_r_at 9.663969
35114_at   7.745817
41041_s_at 8.131253
41759_at   9.489163
> package.version("factDesign")
[1] "1.1.3"

I'm sorry that the values in the previous version were not reported as
such.

Also, I purposely removed the identifiers from the data set because at the
time I put the vignette together, our collaborators were still working on
other biological results using this data.  I will talk to them and see if
it is OK to include the Affy identifiers.  In the meantime, if you are
interested in the biological results of the study, please see Scholtens,
et al.  Analyzing factorial designed microarray experiments, available
online at the Journal of Multivariate Analysis (Articles in Press).

Denise



On Tue, 4 May 2004, Claire Wilson wrote:

> Dear all,
> I have been working through the factDesign vignette and it appears that
> the probeset identifiers have been lost from the expression set and also
> that the expression calls appear to not be in log2 form as indicated in
> the vignette(code shown below)...thanks for any help, claire
>
> > library(affy)
> Welcome to Bioconductor
>          Vignettes contain introductory material.  To view,
>          simply type: openVignette()
>          For details on reading vignettes, see
>          the openVignette help page.
>
> Synching your local package management information ...
> Packages which have been added/updated:
>         estrogen
> > library(factDesign)
> > data(estrogen)
> >  estrogen
> Expression Set (exprSet) with
>         500 genes
>         8 samples
>                  phenoData object with 2 variables and 8 cases
>          varLabels
>                 ES: absence/presence of estrogen
>                 TIME: 10/48 hours
> > exprs(estrogen)[1:10,]
>           [,1]     [,2]     [,3]     [,4]     [,5]     [,6]      [,7]
> [,8]
>  [1,]  787.583  794.075  794.572  711.025  730.022  703.197   796.159
> 760.515
>  [2,]  435.335  513.685  548.721  580.833  518.279  632.801   581.357
> 688.602
>  [3,]  197.784  196.131  184.991  156.459  243.296  219.666   182.644
> 152.647
>  [4,] 1057.410 1099.750  963.088 1094.110 1152.180 1446.360  1102.990
> 1509.770
>  [5,]  452.775  436.912  483.615  447.999  444.369  444.443   540.446
> 537.549
>  [6,] 1175.560 1054.800 3445.030 3906.160  674.682  474.879   998.373
> 901.746
>  [7,]  914.076  823.871  729.431  703.935  376.056  282.645   439.117
> 465.587
>  [8,] 7321.400 6809.660 8195.580 7342.840 6739.340 4984.460 15798.700
> 13363.800
>  [9,]  306.250  275.993  295.424  240.055  183.667  308.580   232.570
> 248.121
> [10,]  482.591  473.398  463.318  495.870  493.339  540.374   507.429
> 486.650
> > exprs(estrogen)["34371_at",]
> Error: no dimnames attribute for array
>
> --------------------------------------------------------
>
>
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__________________________________________________________________________
Denise Scholtens
Department of Biostatistics
Harvard School of Public Health
Office: M1B11, DFCI
Phone: 617.632.4494
dscholte at hsph.harvard.edu