Thanks, it was really helpful. Priscila On Thu, Jan 8, 2009 at 3:58 PM, Jenny Drnevich <drnevich@illinois.edu>wrote: > Hi Priscila, > > The robustspline method for normalization has nothing to do with the > lmFit(method="robust"). lmFit can either fit the model using a least squares > regression or a robust regression, which down-weights replicates that are > different from the other replicates. Whether or not to use > lmFit(method="robust") doesn't depend on which normalization method you use, > but rather (IMO) how many replicates you have. If you have a relatively > large number of replicates, say 6 or more, then the robust fitting of the > model may help to remove true outliers from affecting the data. However, if > you only have 3 replicates, as is usual for microarray experiments, using > the robust estimation may remove real variation in your samples and lead to > more false-positives. > > That's my take on the situation... > Jenny > > At 10:49 AM 1/8/2009, Priscila Grynberg wrote: > >> Content-Type: text/plain >> Content-Disposition: inline >> Content-length: 1308 >> >> >> Hi BioCs, >> I have a doubt about this function. >> >> I'm working with a two-channel dye-swap microarray experiments. After >> testing all normalization methods, I conclude that the robustspline method >> was the best for my data. After normalizing, I did the statistical >> analysis >> using the lmFit and eBayes functions. >> >> My commands were: >> >> fit <- lmFit(MA, design, ndups=2, spacing=12, cor=corfit$consensus) >> >> fit2 <- eBayes(fit) >> >> Everything worked just fine. However, I read the lmFit help and a doubt >> came >> up: >> >> >> lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation,w eights=NULL, >> method="ls",...) >> >> method: character string, "ls" for least squares or "robust" for robust >> regression >> >> Then, I repeat the same commands, but changing the parameter "method", >> since >> I used the robustspline method for normalization. I got different top 100 >> genes most differentially expressed. And now I really confused. I don't >> know >> what to do with this "method" parameter. >> >> I hope someone can explain to me! >> >> Thanks, >> >> Priscila >> >> >> >> >> -- >> Priscila Grynberg, B.Sc., M.Sc. >> Doutoranda em Bioinformática (Bioinformatics D.Sc student) >> Laboratório de Genética Bioquímica >> Universidade Federal de Minas Gerais >> Tel: +55 31 3409-2628 >> CV: http://lattes.cnpq.br/8808643075395963 >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich@illinois.edu > -- Priscila Grynberg, B.Sc., M.Sc. Doutoranda em Bioinformática (Bioinformatics D.Sc student) Laboratório de Genética Bioquímica Universidade Federal de Minas Gerais Tel: +55 31 3409-2628 CV: http://lattes.cnpq.br/8808643075395963 [[alternative HTML version deleted]]