An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061005/ 020c3887/attachment.pl

Hi Wonjong, >I think positive M values means upregulated in 'Treated' (group1), since >I did group1 - group2 'Treated' - 'non-treated'. Is it correct? Yes. If M is positive, that means group1 > group2, and if M is negative, group1 < group2 Cheers, Jenny >Or >negative M value means upregulated in 'Treated'? > >library(limma) >library(affy) >data <- ReadAffy() >eset <- rma(data) >design <- model.matrix(~ -1+factor(c(1,1,1,1,2,2,2,2))) >colnames(design) <- c("group1", "group2") >fit <- lmFit(eset, design) >contrast.matrix <- makeContrasts(group1-group2, levels=design) >fit2 <- contrasts.fit(fit, contrast.matrix) >fit2 <- eBayes(fit2) >topTable(fit2, coef=1, adjust="fdr", sort.by="M", number=10) > > > > >Thank you. > >Wonjong > > > design > group1 group2 >1 1 0 >2 1 0 >3 1 0 >4 1 0 >5 0 1 >6 0 1 >7 0 1 >8 0 1 >attr(,"assign") >[1] 1 1 >attr(,"contrasts") >attr(,"contrasts")$`factor(c(1, 1, 1, 1, 2, 2, 2, 2))` >[1] "contr.treatment" > > > > > > [[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 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 at uiuc.edu