-------------- next part -------------- An embedded message was scrubbed... From: Paul Hammer <paul.hammer@p-t-p.de> Subject: fold change calculation Date: Tue, 19 Feb 2008 19:02:52 +0100 Size: 1895 Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080219/ e187650e/attachment.eml

Paul You don't say which package you're using, but I guess this is simpleaffy? If so, looking at the help page (?get.fold.change.and.t.test) would have told you: "The fold-changes are computed from the average values across replicates. By default this is done using the mean of the unlogged values. The parameter, method allows the mean of the logged values or the median to be used instead. T-tests are always computed with the logged data." Of course, if you don't want to believe the documentation, you can always look at the source code :-) Fold change is simply A-B (if on the log scale), or A/B (if on raw scale). Regards Richard. Paul Hammer wrote: > > > -------------------------------------------------------------------- ---- > > Subject: > fold change calculation > From: > Paul Hammer <paul.hammer at="" p-t-p.de=""> > Date: > Tue, 19 Feb 2008 19:02:52 +0100 > To: > Sean Davis <sdavis2 at="" mail.nih.gov=""> > > To: > Sean Davis <sdavis2 at="" mail.nih.gov=""> > > > dear members, > > could anyone explain or give me the exactly formula of the fold change > calculation? > > R code > ------------------------------------- > > get.fold.change.and.t.test(rma.affy[PDE1A_exon_probesets], > "tissue", c("prostate", "breast"), method="logged") > > > An object of class PairComp > > prostate breast > 2590606 6.237610 4.900560 > 2590612 7.878071 6.961996 > 2590628 4.065403 3.468860 > 2590599 3.854438 3.560036 > 2590615 4.806831 4.309884 > 2590586 1.102444 1.214922 > 2590618 3.314213 3.310029 > 2590608 4.184283 2.767696 > 2590611 5.382736 4.669508 > 2590601 2.871831 2.427491 > 2590617 7.057866 6.922251 > 2590591 3.842315 2.792450 > 2590607 4.448152 3.377348 > 2590613 7.148809 6.013015 > 2590645 4.882622 5.073177 > 2590600 2.777127 3.181344 > 2590616 4.407165 4.127747 > 2590619 1.623058 1.946055 > > Slot "fc": > 2590606 2590612 2590628 2590599 2590615 > 2590586 > 1.337049955 0.916074705 0.596543177 0.294402317 0.496947309 > -0.112478340 > 2590618 2590608 2590611 2590601 2590617 > 2590591 > 0.004183895 1.416586498 0.713228192 0.444339972 0.135614697 > 1.049865355 > 2590607 2590613 2590645 2590600 2590616 > 2590619 > 1.070804709 1.135794462 -0.190555504 -0.404217037 0.279418232 > -0.322996530 > > .... > > thanks > paul > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor