Question: Using write.table with output from topTags [was: report a possible bug of edgeR]
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gravatar for Gordon Smyth
7.1 years ago by
Gordon Smyth36k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth36k wrote:
Dear Peter (or Shan Gao), Short answer: You are using an old version of edgeR. You need to either install the current version of edgeR from Bioconductor or, with the version you have, you can use write.table(result$table, etc) instead of write.table(result, etc). Longer answer: This is not an edgeR bug. The topTags results object has been produced correctly. However, when you try to write it to a file using write.table(), you are trying to treat the results object as a data.frame, which it is not. Hence the error message. In the version of edgeR in the most recent Bioconductor release we added a method for coercing TopTags objects to data.frames, to allow people to do exactly what you're doing. Please have a look at the posting guide: http://www.bioconductor.org/help/mailing-list/posting-guide/ It is a good idea to include output from sessionInfo() in any post. Best wishes Gordon > Date: Wed, 8 Feb 2012 16:33:38 -0500 > From: wang peter <wng.peter at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] report a possible bug of edgeR > > i have two group of samples, > each group have 3 biological replicate > library(edgeR) > library(limma) > > raw.data <- read.table("111",row.names=1) > d <- raw.data[, 1:dim(raw.data)[2]-1 > group <- factor(c(rep("sap", 3),rep("vas", 3))) > d <- DGEList(counts = d, lib.size = > c(9893630,11055814,11207084,9663487,11455088,8140053), group = group) > d <- d[rowSums(d$counts) >= length(group)/2,] > > #normalization > d <- calcNormFactors(d) > > #To estimate common dispersion: > d <- estimateCommonDisp(d) > #To estimate tagwise dispersions: > d <- estimateTagwiseDisp(d) > > et <- exactTest(d) > result <- topTags(et, n=dim(d)[1]+1, adjust.method="BH", sort.by="logFC") > write.table(result,file = "DEresult",sep = "\t") > > Error in data.frame(table = list(logConc = c(-30.7452523676841, > -30.9164328563752, : > arguments imply differing number of rows: 92305, 1, 2 > > but write.table(result[1:92304,],file = "DEresult",sep = "\t") can work well > and then result[92305,] can also work well: > > logConc logFC P.Value FDR > UN089145 -16.96614 -4.874874e-05 1 1 > > > another problem is the result file > "table.logConc" "table.logFC" "table.P.Value" "table.adj.P.Val" "adjust.method" "comparison" > "UN038758" -30.7452523676841 -38.5416037522595 1.78446331842105e-37 2.74524811011424e-33 "BH" "sap" > > > "comparison" should include two group name like, "sap" vs "vas" > but why only one name? > > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839 at cornell.edu > Facebook:http://www.facebook.com/profile.php?id=100001986532253 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
edger • 1.3k views
ADD COMMENTlink modified 7.1 years ago by fire1976 wyoming380 • written 7.1 years ago by Gordon Smyth36k
Answer: Using write.table with output from topTags [was: report a possible bug of edgeR]
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gravatar for fire1976 wyoming
7.1 years ago by
fire1976 wyoming380 wrote:
Hi, Could anybody suggest a way of extracting features/genes associated with related clusters from the results file obtained from ConsensusClusterPlus?Any help would be greatly appreciated. Thanks,Som. [[alternative HTML version deleted]]
ADD COMMENTlink written 7.1 years ago by fire1976 wyoming380
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