search for: toptable

Dear R-Help, I am using the function "topTable" from the LIMMA package. To estimate adjusted P-values there are several options (adjust="fdr" , adjust="BH") as shown below: topTable(fit, number = 10, adjust = "BH", fit$Name) I guess any of these options (fdr, BH, etc.) is using a default of FDR=0.0...

...,dd$NZW3T) > akr <- cbind(dd$AKR1C,dd$AKR2C,dd$AKR3C,dd$AKR1T,dd$AKR2T,dd$AKR3T) > bas <- cbind(dd$NZW1C,dd$NZW2C,dd$NZW3C,dd$AKR1C,dd$AKR2C,dd$AKR3C) > # > design<-matrix(c(1,1,1,1,1,1,0,0,0,1,1,1),ncol=2) > fit1 <- lmFit(nzw,design) > fit1 <- eBayes(fit1) > topTable(fit1,adjust="fdr",number=5) M t P.Value B 12222 3679.480 121.24612 7.828493e-06 -4.508864 1903 3012.405 118.32859 7.828493e-06 -4.508866 9068 1850.232 92.70893 1.178902e-05 -4.508889 10635 2843.534 91.99336 1.178902e-05 -4.508890 561 18727.858...

Hi all. I've got a really dumb question for anyone. How do I write the output of a limma analysis (basically the topTable) to a text file? I want to output the topTable for the entire microarray (not really a topTable anymore I suppose..). Thanks for any advice! -Josh

Hi, I am relatively new to R and Bioconductor and am trying to filter the topTable that I generated of differentially expressed genes from my normlized eset file comprised of ~ 40 HG-133A Affy microarrays . I would like to see if particular probesets are represented in this list. Alternatively I would like to generate a topTable of differentially expressed genes using only spec...

Hello, I have just completed an analysis of microarray data using the limma package. The analysis appears to have worked fine. However, when I use the topTable function to get the significant genes, I get the following error: > topTable(fit2,coef=5,adjust="fdr") Error in array(x, c(length(x), 1), if (!is.null(names(x))) list(names(x), : attempt to set an attribute on NULL Here, fit2 was generated by ebayes(fit), and is not empty,...

...gn<- cbind(individual=c(0,0,1,1,2,2,3,3,4,4,5,5), dim1=c(1,0,1,0,1,0,1,0,1,0,1,0),dim2=c(0,1,0,1,0,1,0,1,0,1,0,1)) fit <- lmFit(normdata@maM, design) contrast.matrix<-makeContrasts(dim1vsdim2=dim2-dim1, levels=design) fit2 <- contrasts.fit(fit,contrast.matrix) fiteb <- eBayes(fit2) Toptable <- topTable(fiteb,number = 10600,genelist=maGeneTable(normdata), sort.by="P", resort.by= "M", adjust="BY") write.table(Toptable,file="RNG_Best_10000genes.txt", row.names=FALSE, col.names=TRUE, sep="\t") best regards [[alternative HTML version...

...- cbind(dd$AKR1C,dd$AKR2C,dd$AKR3C,dd$AKR1T,dd$AKR2T,dd$AKR3T) >> bas <- cbind(dd$NZW1C,dd$NZW2C,dd$NZW3C,dd$AKR1C,dd$AKR2C,dd$AKR3C) >> # >> design<-matrix(c(1,1,1,1,1,1,0,0,0,1,1,1),ncol=2) >> fit1 <- lmFit(nzw,design) >> fit1 <- eBayes(fit1) >> topTable(fit1,adjust="fdr",number=5) > M t P.Value B > 12222 3679.480 121.24612 7.828493e-06 -4.508864 > 1903 3012.405 118.32859 7.828493e-06 -4.508866 > 9068 1850.232 92.70893 1.178902e-05 -4.508889 > 10635 2843.534 91.99336 1.178902e-05 -...

Hallo, > fit12<-lmFit(qrg[,1:2]) > t12<-toptable(fit12,adjust="fdr",number=25,genelist=qrg$genes[,1]) > t12 ID logFC t P.Value adj.P.Val B 522 PLAU_OP -6.836144 -8.420414 5.589416e-05 0.01212520 2.054965 1555 CD44_WIZ -6.569622 -8.227938 6.510169e-05 0.01212520 1.944046 Can anyone tell me wha...

...all rows where the Fpval was greated than 0.01. This table is called #fit2readformulttestFp01.txt fit2<-read.table("fit2readyformulttestFp01.txt", header=TRUE, sep="\t") #WORKS write.table(fit2, file="filteredfit2.txt", sep="\t") #WORKS s0vss24<-topTable(fit2,coef="s0vss24",number=3412,adjust.method="BH",p.value=1) write.table(s0vss24,file="s0vss24.txt",sep="\t") s24vss48<-topTable(fit2,coef="s24vss48",number=3412,adjust.method="BH",p.value=1) write.table(s24vss48,file="s24vss4...

Hi R guru coders I wrote a bit of code to add a new column onto a "topTable" dataframe. That is a list of genes processed using the limma package. I used a for loop but I kept feeling there was a better way using a more vector oriented approach. I looked at several commands such as "apply", "by" etc but could not find a good way to do it. I have th...

...2,2,3,3,3))) colnames(design) <- c("control", "three", "six") fit <- lmFit(x, design) meanSdPlot(x) contrast.matrix <- makeContrasts(three-control, six-control, levels=design) fit2 <- contrasts.fit(fit, contrast.matrix) fit2 <- eBayes(fit2) #### top list topTable(fit2, coef=1, adjust="BH", number=20, sort.by="M") library(hgu133plus2.db) u<-mget(row.names(fit2),hgu133plus2SYMBOL) How can I produce a topTable result with according gene names, somehow I do not understand the genelist argument? Next, I would like to produce a standard c...

...gt;>>> "GS" == Gordon K Smyth <smyth@wehi.edu.au> >>>>> on Sat, 8 Jan 2005 01:11:30 +1100 (EST) writes: <.............> GS> p.adjust() unfortunately gives incorrect results when GS> 'p' includes NAs. The results from topTable are GS> correct. topTable() takes care to remove NAs before GS> passing the values to p.adjust(). There's at least one bug in p.adjust(): The "hommel" method currently does not work at all with NAs (and I have an uncommitted fix ready for this bug). OTOH, the current...

..." to try and separate the columns in excel, everything just stays in one column. how do i get them all into separate columns (it did this before but i can't figure out what's different between this time exporting and other times when i enter the same thing) example: > write.table(topTable(fit2, coef=3, adjust="fdr", > sort.by="B",number=50000), file="preterm_parturient.xlsx", row.names=F, > sep="/t") what about this command wont let the columns get separated? -- View this message in context: http://r.789695.n4.nabble.com/Separating-...

...ge to create 2 contrasts for my data and then calculating the vennCounts of the decideTests from the contrast.fit to be able to create venn Diagrams. The code works fine but the summary(results) shows zeros for all i.e. no gene were up regulated or downregulated. This is not true for my data since toptable output shows Log fold change greater than > 2. I am certain it is a small glitch somewhere at my end that i get zero counts for my summary(decideTests). Please find below my code and i would really appreciate any help here at all. Thanks, Ekta ## R Script ### > numGenes <- nrow(eset) &gt...

...<- c('ndd1_1.txt','ndd1_2.txt','ndd1_3.txt'); RG=read.maimages(files,"arrayvision",sep="\t"); #Normalisation MA=normalizeWithinArrays(RG); #plotPrintTipLoess(MA); #Fit Linear model and Empirical Bayes method fit=lmFit(MA); fit <- eBayes(fit) ; res=topTable(fit,sort.by="P",number=7200); hist(res$P.Value,breaks=50); The error message I get is : Read ndd1_1.txt Read ndd1_2.txt Read ndd1_3.txt Error in switch(method, loess = { : Layout argument not specified I then created a layout file and added in the following code, but I still got the sa...

Hallo, how can I store a variable as a tab-delimited txt-file? I crated a variable with the following commands: > fit12<-lmFit(qrg[,1:2]) > t12<-toptable(fit12,adjust="fdr",number=25,genelist=qrg$genes[,1]) > t12 ID logFC t P.Value adj.P.Val B 522 PLAU_OP -6.836144 -8.420414 5.589416e-05 0.01212520 2.054965 1555 CD44_WIZ -6.569622 -8.227938 6.510169e-05 0.01212520 1.944046 767 CD44_WIZ -8.16431...

...vels(targs) > fit<-lmFit(eset.rma,design) > cont.wt<-makeContrasts("treatment1-control","treatment2-control",level > s= > design) > fit2<-contrasts.fit(fit,cont.wt) > fit2.eb<-eBayes(fit2) > testconts<-classifyTestsF(fit2.eb,p.value=0.01) > topTable(fit2.eb,coef=2,n=300) > topTable(fit2.eb,coef=1,n=300) > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor &g...

...<- sapply(lookUp(probeList, 'lumiHumanAll.db', 'GENENAME'), function(x) x[1]) fit$genes <- data.frame(ID= probeList, geneSymbol=geneSymbol, geneName=geneName, stringsAsFactors=FALSE) } ## print the top 10 genes print(topTable(fit, coef='95:5-100:0', adjust='fdr', number=10)) ## get significant gene list with FDR adjusted p.values less than 0.01 p.adj <- p.adjust(fit$p.value[,2]) sigGene.adj <- probeList[ p.adj < 0.01] ## witho...

...Fit(xen1dataeset,design) # Fit linear model based on the design matrix contrast.matrix<- makeContrasts(B_crp- A_xen) # define contrast matrix fit2<-contrasts.fit(fit,contrast.matrix) # calculate contrast fit3<-eBayes(fit2) # Calculate B and P-values for contrast crpMxen<-topTable(fit3,coef=1,number=22690,adjust.method="BH",sort.by='B') [[alternative HTML version deleted]]

...). MA is an object of class marrayNorm, below is what I did. >design <- c(1,-1,1,-1,1) >cor <- duplicateCorrelation(MA,design,ndups=3) >cor$consensus.correlation [1] 0.506 >fit <- lmFit(MA,design,ndups=3,correlation=cor$consensus.correlation) >fit <- eBayes(fit) >topTable(fit,n=20,adjust="fdr") The result is, ID M A t P.Value B 348 -1.3 10.8 -3.98 0.577 -4.47 371 -1.91 11.5 -3.36 0.577 -4.47 172 -2.56 13.4 -3.36 0.577 -4.47 273 -0.98 10.3 -3.22 0.577 -4.48 ... It seems this is no evidence of differential expression. But if I use the first three slides to...