Question: Top gene list
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13.1 years ago by
daphne mouzaki RI80 wrote:
Hi and thanks for your response, actually topTable and Write.fit works if the object that I have is a MArrayLM object but. The problem is that I have an object "Bgene" which is a list and includes all the columns of interest.I am sorry that I wasn't clear.I have already generated the results but I also tried decideTests in case I could generated them in an other way to get all the FDRs and fold changes for each gene. > class(Bgene) [1] "list" > names(Bgene) [1] "ttAll" "DownSameUp" > names(Bgene$ttAll) [1] "T11" "T3" "T19" "T19_T11" > names(Bgene$ttAll[1]) [1] "T11" > names(Bgene$ttAll[[1]]) [1] "Row" "Column" "Block" "Name" "ID" [6] "Reps" "ARKcloneID" "Status" "M" "A" [11] "t" "P.Value" "adj.P.Val" "B" "FoldChange" [16] "FDRmax" "FDR" "FDRup" "FDRlow" For example, I want to get all the FDr for time point T11 with the respective gene name FDR11<-(Bgene$ttAll[[1]])$FDRmax the problem is that I don't get the respective gene names automatically when I do that and when I assign rownames(FDR)<-sort(unique(MA$genes\$ARKcloneID)) I get an error message that I assign it to something with no dimension which is true because it is not a matrix but a list!! Cheers, Daphne -----Original Message----- From: Giovanni Coppola [mailto:gcoppola@ucla.edu] Sent: 13 September 2006 17:40 To: daphne mouzaki (RI) Cc: Bioconductor list Subject: Re: [BioC] topTable gene list Hi Daphne, perhaps ?write.fit does what you want. Best Giovanni On Sep 13, 2006, at 7:13 AM, daphne mouzaki ((RI)) wrote: > hi, > > I have generated a list of significant genes for 3 time points > separately using the function "decideTests"in Limma package.Using this > function I generated foldchanges and FDR for every gene using method > Benjamini and Hochberg ("BH") and p.value=0.05. > I was wondering if it is possible to generate all the FDR and > foldchanges with the respective gene name for every time point. > I tried changing the cut-off to 1 in order not to exclude anything and > the method set to the function "decideTests" changed to "none" but it > doesn't work. > Could you recommend any other possible ways? > > I would appreciate any help, > > Daphne > > _______________________________________________ > 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
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