You still need to indicate the biorep and use it as a block, even if only one biorep has a replicate. --Naomi At 09:55 PM 9/21/2009, Marcelo Laia wrote: >Hi, > >On the limma usersguide I found the example: > >FileName Cy3 Cy5 >File1 wt1 mu1 >File2 wt1 mu1 >File3 wt2 mu2 >File4 wt2 mu2 > >where two wild-type and two mice from the same mutant strain are >compared using two arrays for each pair of mice. > > > biolrep <- c(1, 1, 2, 2) > > corfit <- duplicateCorrelation(MA, ndups = 1, block = biolrep) > > fit <- lmFit(MA, block = biolrep, cor = corfit$consensus) > > fit <- eBayes(fit) > > topTable(fit, adjust = "BH") > >I have something like this, but, in my case, I have: > > >FileName Cy3 Cy5 >File1 pra1 banha1 >File2 pra1 banha1 >File3 pra2 banha2 >File4 pra3 banha3 > >banha is my reference and pra is my tester. > >Only the two first is technical replicates. The others two are >biological replicates. > >How I could dealing a design for my situation? > >Thank you very much. > > >-- >Marcelo Luiz de Laia >Universidade do Estado de Santa Catarina >UDESC - www.cav.udesc.br >Lages - SC - Brazil >Linux user number 487797 > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111