Hi Eva, Using VST instead of log2 is for the purpose of variance stabilization. Basically the variance will be close to independent of amplitude after VST transformation. The VST will be very close to log2 in the middle or high expression range. There is a function called "inverseVST", which inverse-tranforms the data into raw scale. So you can calculate the fold-change by dividing them. However, you need to be careful for the high fold-change when one expression value is low. Pan On 9/3/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Date: Tue, 2 Sep 2008 15:18:33 +0200 > From: " Mgr. Eva Budinsk? " <budinska at="" iba.muni.cz=""> > Subject: [BioC] How to interpret the vst transformation of illumina > expression data? > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <200809021318.m82DIhZH018743 at minas.ics.muni.cz> > Content-Type: text/plain > > Dear all, > > > > I am analyzing illumina data and I treat a "little" problem. If I use vst > transformation as proposed by Simon Lin and Pan Du for normalization, I have > a problem with interpretation of these values. > > I have 5 clinical groups, from which one is represents controls. If I apply > log2 transformation, I can simply subtract let's say median of control group > from all values and thus obtain a kind of ratio representing the relative > fold change in expression. If the biologists are interested in "real", not > logged expression, I can derive it using the 2^ function to the logarithm of > value of relative fold change (I know this is a bit tricky, but for > informative purposes still usable). > > But when using vst, where arcsinh is used, this task is not so simple, > especially for relative fold change in comparison to control. > > How do you treat this problem? > > > > Thank you very much. > > > > Eva > > > > ********************************************* > Eva Budinsk?, M.Sc. > Institute of Biostatistics and Analyses > Faculty of Science and Faculty of Medicine > Masaryk University > Kamenice 126/3, 625 00, Brno, Czech Republic > ---------------------------- > Tel.: +420 549 493 929 > Fax.: +420 549 492 855 > Mobile: +420 774 206 332 > email: budinska at iba.muni.cz > *********************************************