A related question: Does limma algorithms for dye swap use "weights" for dye flip arrays if not every sample had dye swap replication? For example there are 3 normal vs. tumor arrays, but only one array with different dye-orientation. thanks, JJ --On Thursday, January 24, 2008 4:08 PM +0000 Claus-Dieter Mayer <claus at="" bioss.ac.uk=""> wrote: > Hi Sally, > > What you have done (averaging across the dye-flips) is basically ok, as > the information you loose by doing that only concerns technical > variability. The more sophisticated way of doing things would be to > include all arrays, but to change your limma analysis by > a) adding a dye effect (cf. limma tutorial) > b) adding a block effect that informs the analysis about which arrays > are technical replicates (dye-flips), that analyse the same biological > samples (again see the limma tutorial for details). > > In addition to your treatment effect this analysis will give you > information about gene-specific dye-effects and the correlation between > the two dye-flips. Both of these might not be relevant to the biological > question of interest, but be helpful from a quality control perspective. > If you average the dye-flips you eliminate the gene-specific dye- effect > (which is good), but you also loose the information about it. Equally > you give up the information about the technical array to array (+dye > flip)-variation. The fold-changes you estimate for your biological > effect of interest will be identical for both approaches but p-values > etc will differ slightly. From the point of statistical power both > approaches should be similar as far as I can see (and others may correct > me if I overlooked any subtle points here). > > Best Wishes > > Claus > > > > Sally wrote: >> My question is about handling dye flips in Limma. >> >> In my experiment I did a dye flip for each comparison. When I finished >> the preprocessing I averaged the M values of the two dye flip arrays.Now >> I am fitting a linear model. Should I have averaged the dye flips >> before, or should the dye flips be incorporated in the linear model? >> >> Sally Goldes >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> >> >> >> >> >> >> Click link below to report this email as spam. >> https://www.mailcontrol.com/sr/ubMazK5f8H7cohtw78djyfAVCukN02RG8Mra HiLp2 >> brog64sJZMbax70VQcaVVh5T7KYBPDklBRfAchUXJwv+Q== >> >> >> > > -- > ******************************************************************** ***** > ********** Dr Claus-D. Mayer | http://www.bioss.ac.uk > Biomathematics & Statistics Scotland | email: claus at bioss.ac.uk > Rowett Research Institute | Telephone: +44 (0) 1224 716652 > Aberdeen AB21 9SB, Scotland, UK. | Fax: +44 (0) 1224 715349 > > _______________________________________________ > 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 ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104 University of Chapel Hill Chapel Hill, NC 27599 Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at email.unc.edu