User: Silvia

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Silvia0
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Posts by Silvia

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Answer: A: Unexpected results in the dba.report output files
... Thanks a lot Rory for looking into this. However, after having a second look at your reply I got a bit confused... You said that the error of writing FDR=1 to the output file happens for some sites that have low p-values (did you mean 'high', btw?). The p-value in the example above corresponding to ...
written 21 days ago by Silvia0
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Unexpected results in the dba.report output files
... Hi, I get unexpected results from the dba.report output, with some FDR values being 1. I also see some inconsistencies between that output and the underlying data passed to that function. For example, this is a part of the dba.report output, called using the command dba.report(db_analysis, contrast= ...
diffbind written 4 weeks ago by Silvia0
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Legend for Gviz annotation track?
... Hi, I need to generate a Gviz plot with an annotation track so full of features that, instead of displaying their (long) names in the corresponding arrow shapes, I have to use the option groupAnnotation="group" and just show a number. Is there some way of showing a legend next to the plot with the ...
gviz legend written 8 weeks ago by Silvia0
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Maftools required fields do not match with vignette
... Hi, I just tried to load my MAF file with maftools, but although the vignette states that the required fields are only 7 (Hugo_Symbol, Chromosome, Start_Position, End_Position, Variant_Classification, Variant_Type and Tumor_Sample_Barcode), I got the following error messages: Error in validateMaf ...
maftools written 4 months ago by Silvia0 • updated 4 months ago by anand_mt60
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Venn diagram using contrasts in DiffBind
... Hi Rory, I was trying to plot, using DiffBind_2.2.12, a Venn diagram for the following contrast (the only one present in my DBA object): 1 Contrast: Group1 Members1 Group2 Members2 DB.edgeR 1 CondA 3 CondB 3 64883 ...which I generated using these commands: > db_analysis ...
diffbind written 5 months ago by Silvia0 • updated 5 months ago by Rory Stark2.1k
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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 7 months 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 7 months 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 2.9 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 3.0 years ago by Silvia0 • updated 3.0 years ago by Martin Morgan ♦♦ 20k
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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 3.0 years ago by Silvia0 • updated 2.9 years ago by Rory Stark2.1k

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