User: veronique.storme

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Posts by veronique.storme

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Comment: C: Diffbind: getting the raw reads
... Dear all, I found the answer myself. When I ask for  dba.count(prol.5, peaks=NULL, score=DBA_SCORE_READS_MINUS) I can see that when all negative values are put to 1, I obtain the same reads as in  de.5.edger$contrasts[[1]]$edgeR$counts[1:5,] Veronique ...
written 5 months ago by veronique.storme0
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Diffbind: getting the raw reads
... Dear Rory, I found the solution to my previous questions. However, now I am comparing the results from the available edgeR analysis with the robust edgeR pipeline with QL method based on raw read counts. This is the pipeline that I want to use. I found the raw read counts by reads.5 = dba.count(p ...
edger diffbind raw reads written 5 months ago by veronique.storme0
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Answer: A: ChIPseq diffbind merging peaks
... Dear Rory, Thanks a lot for your time and effort, this was really helpful, Veronique ...
written 6 months ago by veronique.storme0
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Comment: C: ChIPseq diffbind merging peaks
... Dear Rory, I emailed the DBA objects to you last friday. I hope I used the correct email adress. Thank you for your time.  Veronique ...
written 7 months ago by veronique.storme0
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ChIPseq diffbind merging peaks
... Dear, I am new to differential ChIPseq analysis. One condition has 6 biological replicates and the other 3. I did not perform the experiment, I just perform the analysis. I started with loading the data: prol.10 = dba(sampleSheet="macs10_30.csv") This resulted in a total of 7602 peaks with 47 pr ...
diffbind merging_peaks written 7 months ago by veronique.storme0
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Comment: C: edgeR quasi-likelihood dispersion estimates
... Dear Gordon, I not only wish to use the software, I also want to understand the models behind it. I have read all the literature behind it and like to understand what exactly is happening. I read about this variance function and was wondering why it was never calculated, but indeed - if I understand ...
written 8 months ago by veronique.storme0
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Comment: C: edgeR quasi-likelihood dispersion estimates
... Thanks a lot! And the LRT test and the QL F-test only depend on the QL gene-wise dispersion (the posterior variance, object var.post in edegR) (as proven by McCullagh 1983) ? ...
written 8 months ago by veronique.storme0
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edgeR quasi-likelihood dispersion estimates
... Dear, I am using the (robust) QL pipeline in edgeR with following lines of code > estimateDisp > glmQLFit I understand that with this pipeline, only the NB trended dispersion is used from the estimateDisp function, and that glmQLFit estimates QL gene-wise dispersions using the empirical Ba ...
edger written 8 months ago by veronique.storme0 • updated 8 months ago by Aaron Lun16k

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