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 Showing results 1 to 9 of 9 Search took 0.00 seconds. Search: Posts Made By: EVELE
 Forum: Bioinformatics 02-18-2019, 02:20 PM Replies: 22 Views: 5,548 Posted By EVELE Hi, Sorry for the resurrection of such old... Hi, Sorry for the resurrection of such old dialogues but I am quite confused. I was thinking of doing a time-course analysis (as Assa did) having only 1 condition , 4 time points and 3 replicates...
 Forum: RNA Sequencing 10-01-2015, 07:33 AM Replies: 0 Views: 1,132 Posted By EVELE DESeq2*: Dispersion in a DESeq analysis with design=~group Hello, I make a differential expression analysis between treated samples (factors) and untreated (controls) at different states (vegetative, early, inter, late). The problem is that I lack...
 Forum: RNA Sequencing 09-16-2015, 08:41 AM Replies: 5 Views: 1,443 Posted By EVELE In the manual link I sent, it goes like that: ... In the manual link I sent, it goes like that: Wald tests for the log2 fold changes at individual time points can be investigated using the test argument to results: res30 <- results(ddsTC,...
 Forum: RNA Sequencing 09-16-2015, 07:35 AM Replies: 5 Views: 1,443 Posted By EVELE Actually when you don't put test="Wald" I can see... Actually when you don't put test="Wald" I can see that it is a LRT applied and we get LRT pvalues while when putting test="Wald" it is the Wald test pvalues we obtain. I don't know which approach...
 Forum: RNA Sequencing 09-16-2015, 07:15 AM Replies: 5 Views: 1,443 Posted By EVELE It is not the same. I can see differences when... It is not the same. I can see differences when I apply both ways to my data. Common part of code: > times=factor(c(1,rep(2,2),rep(3,2),0,1,rep(2,2),rep(3,2),0), levels=c(0,1,2,3)) > condition =...
 Forum: RNA Sequencing 09-16-2015, 03:51 AM Replies: 5 Views: 1,443 Posted By EVELE Use of test="Wald" in the results of a time-course experiment Hi all, Concerning the example of the manual : http://bioconductor.org/help/workflows/rnaseqGene/#time in the "Time Course Experiments" paragraph, library("fission") data("fission") ddsTC...
 Forum: RNA Sequencing 08-24-2015, 06:46 AM Replies: 0 Views: 1,047 Posted By EVELE DESEQ2: Which of the following 2 contrast methods does what I want ? Hi all, I have 2 time course experiments. For the first experiment I have 5 treated samples (1 for the vegetative stage with no replicates, 2 replicates for the early stage of autogamy and...
 Forum: Bioinformatics 06-30-2015, 01:16 AM Replies: 3 Views: 1,579 Posted By EVELE Hi Michael, First of all many thanks for... Hi Michael, First of all many thanks for your prompt answer. I tried to apply your suggestions. As I am not sure for my understanding and the interpretations I give to my results, I expose (in...
 Forum: Bioinformatics 06-26-2015, 02:12 AM Replies: 3 Views: 1,579 Posted By EVELE DESEQ2: How to use dispersion estimated from one dataset in another dataset Hi all, I have recently started using DeSeq2 and I would like to know if it is possible to do something like this: I have 3 time course experiments (1 control and 2 treated (A and B)) but I do...
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