User: rbronste

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rbronste10
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Posts by rbronste

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Diffbind Consensus vs Differential peak sets from same count
... Trying to get consensus and differential set from the same dba.count and not sure the best way to parse the two. Here is my command string: BN<- dba(sampleSheet = "Adult_AT_BN.csv", config=data.frame(AnalysisMethod="DBA_DESEQ2",th=.05),peakFormat="narrow") BN_count<- dba.count(BN, score=DBA ...
chipseq diffbind written 11 days ago by rbronste10 • updated 4 days ago by Rory Stark2.0k
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Comment: C: DiffBind masks for counts
... Yes this is the same as the other thread, forgot to remove this one after posting. So yes basically have a sheet with male/female vehicle/treatment so 12 samples with 3 reps each (e.g. 3 replicates for Male Vehicle) and want the counts to only add to matrix if peaks in all 3 replicates for one group ...
written 24 days ago by rbronste10
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Comment: C: DiffBind contrasts issue
... Thanks very much for the help!  Another question, will this setup allow me to look at interactions as I do in DESeq alone with sex:treatment etc? (In addition to pairwise comparisons) ...
written 24 days ago by rbronste10
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DiffBind masks for counts
... Trying to generate replicate masks for the dba.count function from a .csv where I list 3 replicates under DBA_CONDITION. Want to do dba.counts with minMembers = 3 to include only those that are in all 3 of each replicate group for the binding matrix. Any clues on how to do this? Thanks. ...
chipseq diffbind written 4 weeks ago by rbronste10 • updated 25 days ago by Rory Stark2.0k
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DiffBind contrasts issue
... Trying to set up a contrast based on some masks and having some problems. The dba.count looks as follows:  12 Samples, 1054182 sites in matrix (2657422 total):      ID Tissue Factor Condition Treatment Replicate Caller Intervals 1 MBV1 BN1 DR MALE VEHICLE 1 narrow 500000 ...
chipseq diffbind written 4 weeks ago by rbronste10 • updated 25 days ago by Rory Stark2.0k
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Comment: C: samtools loading in R
... I am using Mac OS, unfortunately no way around the R package I am using for this task so need to fix this error. ...
written 7 weeks ago by rbronste10
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samtools loading in R
... Hi Using a package that requires samtools and only finding Rsamtools from Bioconductor, have that loaded and getting the following error: sh: samtools: command not found Error in readBAMIndex(bamFile, refgenome = refgenome) :    Cannot run "samtools".  Install "samtools" first! Is there a regular ...
rsamtools samtools written 7 weeks ago by rbronste10 • updated 7 weeks ago by Martin Morgan ♦♦ 20k
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Comment: C: ddCT Package for StepOnePlus qPCR output
... Hi David, wondering if you had any thoughts on my example? Thanks again! ...
written 7 weeks ago by rbronste10
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Comment: C: ddCT Package for StepOnePlus qPCR output
... Hi David, thank you for taking a look, an example is linked below. https://u105647823.dl.dropboxusercontent.com/u/105647823/ag_070617_data.xls   ...
written 8 weeks ago by rbronste10
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ddCT Package for StepOnePlus qPCR output
... Hi, Trying to figure out a good way to read in raw data off a StepOnePlus machine into the ddCt package? Or if any other solid suggestions for ddCt-type packages with graphical outputs. Thank you. Rob ...
geneexpression qpcr ddct written 8 weeks ago by rbronste10 • updated 8 weeks ago by Zhang, Jitao David100

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