Dear all, I have been working through the factdesign vignette and was wondering why only 500 genes are used. The data given are derived from Affymetrix HGU95av2 chips that have been normalised using RMA. I believe the U95av2 chips measure the abundance of ~12,000 transcripts. Is the filtering of genes from 12,000 to 500 done purely for size reasons and if so how were these 500 selected? If not what criteria were used to select the 500 genes? Many thanks Claire -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

Hi Claire, The 500 probes are a random sample of the 12625 probes available on the U95av2 array. No biological interpretability here - this was done purely for size reasons so that the vignette would run a little faster. Denise On Tue, 4 May 2004, Claire Wilson wrote: > Dear all, > > I have been working through the factdesign vignette and was wondering > why only 500 genes are used. The data given are derived from Affymetrix > HGU95av2 chips that have been normalised using RMA. I believe the U95av2 > chips measure the abundance of ~12,000 transcripts. Is the filtering of > genes from 12,000 to 500 done purely for size reasons and if so how were > these 500 selected? If not what criteria were used to select the 500 > genes? > > Many thanks > > Claire > > -------------------------------------------------------- > > > 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