Dear Tobias, thank you. It would be helpful if you could provide me the file resulting from save(til, file="til.rda") via a download link. I will treat this confidentially if necessary. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Straub ha scritto: > Dear Wolfgang, > > this is how I run vsn: > > ##################################### > library(vsn) > > #get the matrix of raw intensities > d.raw <- as.matrix(til[,5:16]) > > d.norm.old <- vsn(d.raw, subsample=20000) > d.norm.new <- vsn2(d.raw, subsample=20000) > > ##################################### > > I just discovered, that if I don't use subsampling the poblem gets even > worse: > http://www.badongo.com/pic/689985 > > the meanSdPlot (with subsampling) looks like this: > http://www.badongo.com/pic/690005 > > the pairs of my matrix (pre-vsn) looks like this: > http://www.badongo.com/pic/690007 > > If you want I can provide you the complete dataset via a local download > link. > > best wishes > Tobias > > On May 30, 2007, at 6:36 PM, Wolfgang Huber wrote: > >> >> Dear Tobias, >> >> it looks odd indeed, - can you provide me a reproducible script to >> reproduce your problem? As Gordon pointed out earlier, I also need the >> necessary input data (which does not need to be your data, but any sort >> of data that reproduces your problem). >> >> 1. How does the "meanSdPlot" look for "old" and "new" ? >> >> 2. How the "pairs" plot of the 12 matrix columns against each other (see >> man page of geneplotter::smoothScatter for an example how to make it)? >> >> 3. You can always use the old "vsn" function, in spite of the >> deprecation warning it is still there as always and will remain so for a >> while. Of course I hope this kind of problems can be sorted out with the >> new implementation; working hard on it. >> >> Thank you & Best wishes >> Wolfgang >> >> ------------------------------------------------------------------ >> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >> >> >> >> >> Straub ha scritto: >>> Dear all, >>> >>> with the upgrade to bioc 1.5.0 I am facing vsn2. >>> as already discussed in an older thread there are calculation >>> differences. however, in my dataset(s) I get a massive outlier >>> comparing the array means after normalization with old vsn and vsn2. >>> >>> scatterplot here: http://server7.pictiger.com/img/198354/other/vsn- >>> bioc.png >>> >>> my data are six replicates of dual color tiling microarray (193290 >>> spots), i.e. i pass a 193290 x 12 matrix to vsn. >>> >>> i guess that's a bug, is it? >>> >>> Tobias >>> >>> >>> ====================================================================== >>> Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular Biology >>> tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, Germany >>> > > ====================================================================== > Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular Biology > tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, Germany > ====================================================================== >