Hi Wonjong, You should always post your questions back to the list for the archives... You should read through the help for topTable so you can understand what the different arguments will do. In the example code you give, you told it to sort by M, which it will do from largest negative value to largest positive value; this is why the top 10 genes all have negative M values (and they are still all down-regulated in group1). >I sorted saved the longer list and sorted from largest postive, this >time all P value was 1. This doesn't make sense - you should give the code you used instead of a description of what you thought you did. My guess is that you are somehow sorting the genes with significant positive M values to the bottom of the ranking, then not getting these genes due to your number cutoff. To quickly check how many significantly (at fdr p <= 0.05) up-regulated genes there are, try: coded.results <- decideTests(fit2) summary(coded.results) 1's are up-regulated, 0's not significant and -1's down-regulated at fdr p=0.05. Best, Jenny >In this case, does negative mean up regulated in group1? > > > topTable(fit2, coef=1, adjust="fdr", sort.by="M", number=10) > ID M A t P.Value adj.P.Val B >19736 Pf.13_1.328.0_CDS_at -5.47 6.01 -7.56 6.50e-05 2.00e-02 2.30 >18019 AJ290929.1_s_at -5.32 7.35 -3.89 4.59e-03 2.34e-01 -1.97 >20850 Pf.2.3.0_CDS_at -5.21 6.38 -7.09 1.02e-04 2.67e-02 1.86 >20063 Pf.13_1.84.0_CDS_a_at -5.03 4.54 -22.62 1.51e-08 5.74e-05 8.73 >22101 Pf.7.64.0_CDS_a_at -5.03 4.64 -23.24 1.22e-08 5.74e-05 8.84 >18142 K03509.1_RC_x_at -5.00 5.10 -8.62 2.52e-05 1.01e-02 3.19 >21440 Pf.5.22.0_CDS_at -4.96 4.30 -17.30 1.25e-07 2.42e-04 7.50 >18009 AJ290918.1_s_at -4.89 6.87 -5.19 8.29e-04 9.78e-02 -0.23 >22299 Pf.8.290.0_CDS_at -4.83 6.64 -17.24 1.28e-07 2.42e-04 7.48 >18020 AJ290930.1_s_at -4.74 5.51 -6.81 1.35e-04 3.17e-02 1.58 > >-----Original Message----- >From: Jenny Drnevich [mailto:drnevich at uiuc.edu] >Sent: Thursday, October 05, 2006 8:19 AM >To: Wonjong Moon; bioconductor at stat.math.ethz.ch >Subject: Re: [BioC] Limma question: positive M values means upregulated >in 'Treated' in this case? > >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 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