Hi Stephen, I had read that discussion but misunderstood the conclusions. On re- reading it, I think you are correct: filtering on fold change in this situation is bad! Many thanks, Quentin > -----Original Message----- > From: Stephen Henderson [mailto:s.henderson at ucl.ac.uk] > Sent: 23 February 2006 12:36 > To: Quentin Anstee > Cc: bioconductor at stat.math.ethz.ch > Subject: RE: [BioC] Filter on Fold Change > > Hi Quentin > > There has been a similar discussion over the past few days. > The main conclusion being (I think) not to filter based upon > a known contrast in your data. This will bias any multiple > testing corrections you make. > > What you have done so far is OK but if you were going to use > something like limma to fit a linear model to your data it > would be better to fit it all and select the interesting bits > (toptable) based on your contrast afterwards. > > > Stephen Henderson > Wolfson Inst. for Biomedical Research > Cruciform Bldg., Gower Street > University College London > United Kingdom, WC1E 6BT > +44 (0)207 679 6827 > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Quentin Anstee > Sent: 23 February 2006 11:19 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Filter on Fold Change > > Dear List, > > I have used the genefilter package to filter out > uninformative probe sets from my GCRMA normalised affy > experiment as follows. > > f1 <- kOverA(3,6) > f2 <- function(x) (IQR(x) > 0.5) > ff<-filterfun(f1,f2) > wh<-genefilter(esetGCRMA, ff) > mySubSet<-esetGCRMA[wh,] > > I would also like to filter out those genes that have less > than a 2-fold change in expression between any two of my > three study groups *before* I go on to fit a linear model and > test for significant differences. My aim is to test as few > genes as possible to minimise the effect of multiple testing > correction and as I will only follow-up those with at least a > 2-fold change, I would like to filter out the rest as soon as > possible. > > Please can you advise me whether this can be achieved with genefilter. > Also, > any advice on how to script this would also be much > appreciated - I have had a look at the vignettes but can't > find any that describe filtering on fold change although I > see from the list archives that it is commonly done. > > Many thanks, > > Quentin > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > ********************************************************************** > This email and any files transmitted with it are confident...{{dropped}}