User: mforoo1

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mforoo10
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Posts by mforoo1

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Binding site overlaps
... Hello, I have a question about figure 13 in the Diffbind manual.  according to this part (page4, > tamoxifen <- dba(sampleSheet="tamoxifen.csv") :  3 MCF71 MCF7 ER Responsive Full-Media 1 raw 1513  , we have 1513 peaks in MCF71 sample. when we draw the binding site overlaps (figure12), if we ...
diffbind written 5 months ago by mforoo10 • updated 5 months ago by Rory Stark2.1k
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Answer: A: got 0 significant differential bound (DB)
... Thanks a lot. I did the dba.count with summits=75 and also get 0 again. I retrieved all sites by calling dba.report() with th=1 and bCounts=TRUEcalling dba.report() with th=1 and bCounts=TRUE. it is wrierd that i got the same FDR for all sites.         Chr    Start      End  Conc Conc_C Conc_P  Fol ...
written 5 months ago by mforoo10
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Comment: C: got 0 significant differential bound (DB)
... Thanks a lot. I did the dba.count with summits=75 and also get 0 again. I retrieved all sites by calling dba.report() with th=1 and bCounts=TRUEcalling dba.report() with th=1 and bCounts=TRUE. it is wrierd that i got the same FDR for all sites.         Chr    Start      End  Conc Conc_C Conc_P  Fol ...
written 5 months ago by mforoo10
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Comment: C: got 0 significant differential bound (DB)
... I got it, I should put 8. sorry for asking a lot of questions.  ...
written 5 months ago by mforoo10
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Comment: C: got 0 significant differential bound (DB)
... Hello Rory,  Many thanks for your help. I tried the first option but I got the error :  Error in dba(H3K4me3, mask = H3K4me3$masks$C, minOvlerap = 2) :    unused argument (minOvlerap = 2) the second option gave me the peakset, I was wondering how C was specified?  How can I do it for P samples as ...
written 5 months ago by mforoo10
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Answer: A: got 0 significant differential bound (DB)
... I installed version 2.4.3. But I still could not get the DB.  1 Contrast:   Group1 Members1 Group2 Members2 DB.DESeq2 1      C        3      P        3         0 Error in pv.getPlotData(DBA, attributes = attributes, contrast = contrast,  :    Unable to plot -- no sites within threshold Calls: plot ...
written 5 months ago by mforoo10
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Answer: A: got 0 significant differential bound (DB)
... thanks, I am going to install the latest version for finding DB. I have another question:  I have 3 replicates in each condition nad I tried to find the overlap between them. I did the dba.overlap  dba.overlap(H3K4me3, H3K4me3$masks$C, mode=DBA_OLAP_RATE) and I got the result: 1] 41820 24549 1693 ...
written 5 months ago by mforoo10
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Answer: A: got 0 significant differential bound (DB)
... Do you think I should update it to new version to get the DB?   ...
written 5 months ago by mforoo10
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Answer: A: got 0 significant differential bound (DB)
... hello,  thanks for responding to my question. It is  DiffBind_1.16.3. ...
written 5 months ago by mforoo10
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got 0 significant differential bound (DB)
... Hello, I run diffbind to find DB between my two samples( control and phosphate deficiency) with two replicates. i choose deseq2 method for dba.analyzes and I got this:   1 Contrast:   Group1 Members1 Group2 Members2 DB.DESeq2 1      C        3      P        3         0 Error in pv.DBAreport(pv, co ...
diffbind written 5 months ago by mforoo10

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