Dear list, topTable is a convenient function for displaying the top regulated genes in an experiment. topTable is usually applied on a object that is generated after fitting a linear model AND subsequent application of the eBayes funtion (fit3 below). I would like to view the results of a model WITHOUT applying the eBayes function, preferably using topTable. That is, using topTable to summerize the results of fit2 below. Applying topTable as such won't work; apparently a format imposed by the eBayes function is required to have topTable properly work. Even specifying a contrast of interest doesn't work. Therefore, has anyone a suggestion how to summerize the results of the fit2 mentioned below? Thanks, Guido > library(affy) > library(limma) > targets <- readTargets("targets_A23.txt") > > affy.data <- ReadAffy(filenames=targets$FileName) > x.norm <- rma(affy.data) Background correcting Normalizing Calculating Expression > > TS <- paste(targets$Strain, targets$Treatment, sep=".") > TS <- factor(TS, levels=c("WT.Con","WT.WY","KO.Con","KO.WY")) > design <- model.matrix(~0+TS) > colnames(design) <- levels(TS) > fit <- lmFit(x.norm, design) > cont.matrix <- makeContrasts(A=WT.WY-WT.Con, B=KO.WY-KO.Con, levels=design) > > fit2 <- contrasts.fit(fit, cont.matrix) #<<---- how to conviently summerize results of this fit? > > fit3 <- eBayes(fit2) > > topTable(fit3) ID A B AveExpr F P.Value adj.P.Val 13289 1431833_a_at 3.538370 -0.091190845 7.856618 1453.7786 5.084771e-18 1.153734e-13 18706 1450643_s_at 2.847376 0.182291682 7.907519 1234.5101 1.739465e-17 1.620566e-13 17177 1449065_at 4.528581 0.125074564 6.713129 1200.7506 2.142661e-17 1.620566e-13 7120 1422925_s_at 3.149781 -0.007867198 8.072523 895.1004 1.945926e-16 1.103827e-12 7192 1422997_s_at 4.298410 0.090012125 8.311977 837.9040 3.193016e-16 1.448991e-12 13047 1431012_a_at 2.682180 0.228653000 8.911287 785.9448 5.159295e-16 1.698832e-12 6721 1422526_at 2.772829 0.123117132 8.060643 784.2985 5.240997e-16 1.698832e-12 16494 1448382_at 3.386068 0.193350865 9.658716 685.0981 1.442685e-15 3.703026e-12 296 1415965_at 3.749143 0.071163645 5.293939 683.4572 1.468807e-15 3.703026e-12 8911 1424716_at 2.647513 0.370083995 8.453969 665.2223 1.798165e-15 4.080035e-12 > topTable(fit2) Error in topTableF(fit, number = number, genelist = genelist, adjust.method = adjust.method, : F-statistics not available. Try topTable for individual coef instead. > topTable(fit2, coef=1) Error in dim(data) <- dim : attempt to set an attribute on NULL > > sessionInfo() R version 2.11.0 (2010-04-22) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] moe430acdf_2.6.0 limma_3.4.0 affy_1.26.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.11.0 > ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com<http: nutrigene.4t.com=""/> email: guido.hooiveld@wur.nl [[alternative HTML version deleted]]

Hi Guido, topTable for a single coef needs the $t, $p.value and $lods that are created from eBayes. You could manually compute these to be regular t-statistics instead of those from eBayes. See section 10 of the limmaUsersGuide(). Try this (I didn't test it): fit2$t <- fit2$coef/fit2$stdev.unscaled/fit2$sigma fit2$p.value <- 2 * pt(-abs(fit2$t), df = fit2$df.residual) The $lods is harder; if you care about it you'll have to figure out how to duplicate it from the ebayes code by using modified inputs, which is what I did for the $t and $p-value; if you don't care about it but need something for topTable to work, I'd just do: fit2$lods <- fit3$lods HTH, Jenny At 12:51 PM 8/31/2010, Hooiveld, Guido wrote: >Dear list, > >topTable is a convenient function for displaying the top regulated >genes in an experiment. topTable is usually applied on a object that >is generated after fitting a linear model AND subsequent application >of the eBayes funtion (fit3 below). >I would like to view the results of a model WITHOUT applying the >eBayes function, preferably using topTable. That is, using topTable >to summerize the results of fit2 below. Applying topTable as such >won't work; apparently a format imposed by the eBayes function is >required to have topTable properly work. Even specifying a contrast >of interest doesn't work. >Therefore, has anyone a suggestion how to summerize the results of >the fit2 mentioned below? > >Thanks, >Guido > > > library(affy) > > library(limma) > > targets <- readTargets("targets_A23.txt") > > > > affy.data <- ReadAffy(filenames=targets$FileName) > > x.norm <- rma(affy.data) >Background correcting >Normalizing >Calculating Expression > > > > TS <- paste(targets$Strain, targets$Treatment, sep=".") > > TS <- factor(TS, levels=c("WT.Con","WT.WY","KO.Con","KO.WY")) > > design <- model.matrix(~0+TS) > > colnames(design) <- levels(TS) > > fit <- lmFit(x.norm, design) > > cont.matrix <- makeContrasts(A=WT.WY-WT.Con, B=KO.WY-KO.Con, levels=design) > > > > fit2 <- contrasts.fit(fit, cont.matrix) #<<---- how to > conviently summerize results of this fit? > > > > fit3 <- eBayes(fit2) > > > > topTable(fit3) > ID A B AveExpr F > P.Value adj.P.Val >13289 1431833_a_at 3.538370 -0.091190845 7.856618 1453.7786 >5.084771e-18 1.153734e-13 >18706 1450643_s_at 2.847376 0.182291682 7.907519 1234.5101 >1.739465e-17 1.620566e-13 >17177 1449065_at 4.528581 0.125074564 6.713129 1200.7506 >2.142661e-17 1.620566e-13 >7120 1422925_s_at 3.149781 -0.007867198 8.072523 895.1004 >1.945926e-16 1.103827e-12 >7192 1422997_s_at 4.298410 0.090012125 8.311977 837.9040 >3.193016e-16 1.448991e-12 >13047 1431012_a_at 2.682180 0.228653000 8.911287 785.9448 >5.159295e-16 1.698832e-12 >6721 1422526_at 2.772829 0.123117132 8.060643 784.2985 >5.240997e-16 1.698832e-12 >16494 1448382_at 3.386068 0.193350865 9.658716 685.0981 >1.442685e-15 3.703026e-12 >296 1415965_at 3.749143 0.071163645 5.293939 683.4572 >1.468807e-15 3.703026e-12 >8911 1424716_at 2.647513 0.370083995 8.453969 665.2223 >1.798165e-15 4.080035e-12 > > topTable(fit2) >Error in topTableF(fit, number = number, genelist = genelist, >adjust.method = adjust.method, : > F-statistics not available. Try topTable for individual coef instead. > > topTable(fit2, coef=1) >Error in dim(data) <- dim : attempt to set an attribute on NULL > > > > sessionInfo() >R version 2.11.0 (2010-04-22) >i386-pc-mingw32 > >locale: >[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >States.1252 LC_MONETARY=English_United States.1252 >LC_NUMERIC=C LC_TIME=English_United States.1252 > >attached base packages: >[1] stats graphics grDevices utils datasets methods base > >other attached packages: >[1] moe430acdf_2.6.0 limma_3.4.0 affy_1.26.1 Biobase_2.8.0 > >loaded via a namespace (and not attached): >[1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.11.0 > > > > >------------------------------------------------ >Guido Hooiveld, PhD >Nutrition, Metabolism & Genomics Group >Division of Human Nutrition >Wageningen University >Biotechnion, Bomenweg 2 >NL-6703 HD Wageningen >the Netherlands >tel: (+)31 317 485788 >fax: (+)31 317 483342 >internet: http://nutrigene.4t.com<http: nutrigene.4t.com=""/> >email: guido.hooiveld at wur.nl > > > > [[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