User: Silvia

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Silvia0
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Posts by Silvia

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Low FDR for significant peaks in DiffBind output
... Hi Rory, Sorry for the delay of my reply, I've been unwell. Thanks a lot for your suggestions! There was indeed something weird with the read counts, but after I updated both DiffBind (1.16.3 -> 2.2.12) and systemPipeR (1.4.8 -> 1.8.1) the counts finally matched what I saw from the bam file ...
written 4 weeks ago by Silvia0
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Low FDR for significant peaks in DiffBind output
... Hi, I used DiffBind for a collaborator who noticed that, contrary to his expectations, a particular region (which overlaps highly significant (pvalue << 0.001) peaks from MACS2 in each replicate of condition Y) got a very low FDR when compared to condition X (in which there are no peaks from ...
diffbind written 5 weeks ago by Silvia0
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Comment: C: inconsistency between dba.plotVenn and input peaks
... Right, I haven't thought about it... Thanks! ...
written 2.4 years ago by Silvia0
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removing "_" automatically inserted in dba.report filename
... Hi there, I was wondering whether it is possible to remove the symbol _ automatically inserted by dba.report() in the output filename. Even if I specify the option initString='' , the output file will be named _myPrefix.csv. The point is that I would like to create this file in a directory differe ...
diffbind dba.report written 2.5 years ago by Silvia0 • updated 2.5 years ago by Martin Morgan ♦♦ 19k
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inconsistency between dba.plotVenn and input peaks
... Hi there, using dba.plotVenn I realized that the sum of number of peaks that I got in each circle of the Venn diagram is not equal to the number of peaks that I had in my input file. When I went back to the tutorial of the DiffBind package ( http://bioconductor.org/packages/release/bioc/vignettes/D ...
diffbind written 2.5 years ago by Silvia0 • updated 2.5 years ago by Rory Stark1.7k

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