Dear Listers, I have a working Limma script below, but I don't know what the output is comparing. Can anyone give me a clue? Also, you can see from my run that i am having other syntax problems. Thanks, Shawn Script: dataMatrix <- exprs(lumi.N) presentCount <- pData(featureData(lumi.N))$presentCount selDataMatrix <- dataMatrix[presentCount > 0, ] selProbe <- rownames(selDataMatrix) sampleType <- c('1st_litter','WT','2nd_litter','WT','1st_litter','2nd_litter','WT',' 1st_litter') require(limma) design <- model.matrix(~ factor(sampleType)) colnames(design) <- c('1st_litter', '2nd_litter', 'WT') fit <- lmFit(selDataMatrix, design) fit <- eBayes(fit) if (require(lumiMouseV1) & require(annotate)) { geneSymbol <- getSYMBOL(fit$genes$ID, 'lumiMouseV1') fit$genes <- data.frame(fit$genes, geneSymbol=geneSymbol) } topTable(fit, coef='WT', adjust='fdr', number=10) p.adj <- p.adjust(fit$p.value[,2]) sigGene.adj <- selProbe[ p.adj < 0.01] sigGene <- selProbe[ fit$p.value[,2] < 0.001] } Transcript: > dataMatrix <- exprs(lumi.N) > presentCount <- pData(featureData(lumi.N))$presentCount > selDataMatrix <- dataMatrix[presentCount > 0, ] > selProbe <- rownames(selDataMatrix) > sampleType <- c('1st_litter','WT','2nd_litter','WT','1st_litter','2nd_litter','WT',' 1st_litter') > require(limma) [1] TRUE > design <- model.matrix(~ factor(sampleType)) > colnames(design) <- c('1st_litter', '2nd_litter', 'WT') > fit <- lmFit(selDataMatrix, design) > fit <- eBayes(fit) > if (require(lumiMouseV1) & require(annotate)) { + geneSymbol <- getSYMBOL(fit$genes$ID, 'lumiMouseV1') + fit$genes <- data.frame(fit$genes, geneSymbol=geneSymbol) + } > topTable(fit, coef='WT', adjust='fdr', number=10) ID geneSymbol logFC t P.Value adj.P.Val 9576 ooK5UkVej.E737PSw0 Fkbp5 0.6698199 9.658213 6.216342e-06 0.06326372 5398 faEIr_9OZAUBsX0VLk Per2 0.6880751 7.431683 4.825718e-05 0.24555665 9243 oyruyspXqhyohXojdA Arc -1.0021833 -7.023328 7.395032e-05 0.25086413 3875 uefVK.bBeKqfv9XzuQ Xbp1 0.4280023 6.613818 1.155933e-04 0.25790396 9581 HAyFSJK.n9pHhIQJS4 Dusp1 -1.0741752 -6.530455 1.269007e-04 0.25790396 6386 lKF2iniB8HnghGhHXk Slc2a1 0.7937010 6.371030 1.520511e-04 0.25790396 9717 iUEl382FlILs4VFkFk Tekt4 0.3838363 6.036845 2.244065e-04 0.32625504 8764 otfSbQ70_07x405Ptg Fos -1.0311305 -5.863374 2.762056e-04 0.35136802 8467 r7fv79XdQPfX3_5FeU Sox9 -0.6741969 -5.203197 6.317984e-04 0.71442364 7276 HbaB_NS3aeHQg7ogic Polr3e 0.3346411 5.079054 7.431893e-04 0.75634378 B 9576 -0.6906876 5398 -1.0774567 9243 -1.1777686 3875 -1.2909444 9581 -1.3156866 6386 -1.3647262 9717 -1.4753395 8764 -1.5372394 8467 -1.8044508 7276 -1.8608493 > p.adj <- p.adjust(fit$p.value[,2]) > sigGene.adj <- selProbe[ p.adj < 0.01] > sigGene <- selProbe[ fit$p.value[,2] < 0.001] > } Error: syntax error >

Shawn Westaway wrote: > Dear Listers, > I have a working Limma script below, but I don't know what the output > is comparing. Can anyone give me a clue? Also, you can see from my run > that i am having other syntax problems. > Thanks, > Shawn > > Script: > > dataMatrix <- exprs(lumi.N) > presentCount <- pData(featureData(lumi.N))$presentCount > selDataMatrix <- dataMatrix[presentCount > 0, ] > selProbe <- rownames(selDataMatrix) > sampleType <- > c('1st_litter','WT','2nd_litter','WT','1st_litter','2nd_litter','WT' ,'1st_litter') > require(limma) > design <- model.matrix(~ factor(sampleType)) > colnames(design) <- c('1st_litter', '2nd_litter', 'WT') This is almost certainly wrong. Your model matrix will have an intercept, so the first column will be 1st_litter, but the second will be 2nd_liter - 1st_litter, and the third will be wt - 1st_litter. Probably you want to compare the litters to wt, so you might do something like sampleType <- factor(c('1st_litter','WT','2nd_litter','WT','1st_litter','2nd_litter' ,'WT','1st_litter'), levels=c("WT","1st_litter","2nd_litter")) Now the second coefficient will be 1st_litter - wt and the third coefficient will be 2nd_litter - wt. > fit <- lmFit(selDataMatrix, design) > fit <- eBayes(fit) > if (require(lumiMouseV1) & require(annotate)) { > geneSymbol <- getSYMBOL(fit$genes$ID, 'lumiMouseV1') > fit$genes <- data.frame(fit$genes, geneSymbol=geneSymbol) > } > topTable(fit, coef='WT', adjust='fdr', number=10) > p.adj <- p.adjust(fit$p.value[,2]) > sigGene.adj <- selProbe[ p.adj < 0.01] > sigGene <- selProbe[ fit$p.value[,2] < 0.001] > } That is an extra '}', which causes the error below. You also appear to be just doing things here, and I don't see what the goal is. Maybe you can say what you are trying to do and then we could give some advice. Best, Jim > > > Transcript: > > >>dataMatrix <- exprs(lumi.N) >>presentCount <- pData(featureData(lumi.N))$presentCount >>selDataMatrix <- dataMatrix[presentCount > 0, ] >>selProbe <- rownames(selDataMatrix) >>sampleType <- > > c('1st_litter','WT','2nd_litter','WT','1st_litter','2nd_litter','WT' ,'1st_litter') > >>require(limma) > > [1] TRUE > >>design <- model.matrix(~ factor(sampleType)) >>colnames(design) <- c('1st_litter', '2nd_litter', 'WT') >>fit <- lmFit(selDataMatrix, design) >>fit <- eBayes(fit) >>if (require(lumiMouseV1) & require(annotate)) { > > + geneSymbol <- getSYMBOL(fit$genes$ID, 'lumiMouseV1') > + fit$genes <- data.frame(fit$genes, geneSymbol=geneSymbol) > + } > >>topTable(fit, coef='WT', adjust='fdr', number=10) > > ID geneSymbol logFC t P.Value > adj.P.Val > 9576 ooK5UkVej.E737PSw0 Fkbp5 0.6698199 9.658213 6.216342e-06 > 0.06326372 > 5398 faEIr_9OZAUBsX0VLk Per2 0.6880751 7.431683 4.825718e-05 > 0.24555665 > 9243 oyruyspXqhyohXojdA Arc -1.0021833 -7.023328 7.395032e-05 > 0.25086413 > 3875 uefVK.bBeKqfv9XzuQ Xbp1 0.4280023 6.613818 1.155933e-04 > 0.25790396 > 9581 HAyFSJK.n9pHhIQJS4 Dusp1 -1.0741752 -6.530455 1.269007e-04 > 0.25790396 > 6386 lKF2iniB8HnghGhHXk Slc2a1 0.7937010 6.371030 1.520511e-04 > 0.25790396 > 9717 iUEl382FlILs4VFkFk Tekt4 0.3838363 6.036845 2.244065e-04 > 0.32625504 > 8764 otfSbQ70_07x405Ptg Fos -1.0311305 -5.863374 2.762056e-04 > 0.35136802 > 8467 r7fv79XdQPfX3_5FeU Sox9 -0.6741969 -5.203197 6.317984e-04 > 0.71442364 > 7276 HbaB_NS3aeHQg7ogic Polr3e 0.3346411 5.079054 7.431893e-04 > 0.75634378 > B > 9576 -0.6906876 > 5398 -1.0774567 > 9243 -1.1777686 > 3875 -1.2909444 > 9581 -1.3156866 > 6386 -1.3647262 > 9717 -1.4753395 > 8764 -1.5372394 > 8467 -1.8044508 > 7276 -1.8608493 > >>p.adj <- p.adjust(fit$p.value[,2]) >>sigGene.adj <- selProbe[ p.adj < 0.01] >>sigGene <- selProbe[ fit$p.value[,2] < 0.001] >>} > > Error: syntax error > > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.