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 -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

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 > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use o...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > ______________________________________________________________________ ____ Denise Scholtens Department of Biostatistics Harvard School of Public Health Office: M1B11, DFCI Phone: 617.632.4494 dscholte@hsph.harvard.edu