Hi Jaana, You can find all the R script of the Vignette in the doc sub- directory of the lumi package. For example, the R script of lumi.pdf is included in the lumi.R file. You can find the directory by typing the following command in the R console: system.file('doc', package='lumi') Tell me if there is anything unclear. Pan On 3/2/09 1:46 PM, "Jaana Hartiala" <hartiala@usc.edu> wrote: > Dr. Du, > I'm reading the "Using lumi, a package processing Illumina Microarray" and I > noticed one the of R-codes (for Figure 13) is missing the last part on page > 19: >> > ## compare the log2 and VST transform >> > matplot(log2(trans$untransformed), trans$transformed, main='compare VST and >> log2 transform', > > Would you be kind enough to advise what the complete code should be? > [[alternative HTML version deleted]]