User: meisan406

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meisan4060
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Posts by meisan406

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Comment: C: Inconsistent peak width with DiffBind "summit" function
... Hi Rory, Thank you for the clarification. I think the fix you are planning would fit in better with the goal of the "summit" function. I look forward to the new release. Thanks, Mei San ...
written 2.0 years ago by meisan4060
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Inconsistent peak width with DiffBind "summit" function
... This is a question on the "summit" function in DiffBind. I would like to generate a set of consensus peaks with width of 201bp, centered around the peak summit. The codes I used were: dba.object <- dba( sampleSheet = metadata, peakCaller="bed", scoreCol=5, bRemoveM=TRUE, bLowerScoreBetter=TRUE ...
diffbind written 2.0 years ago by meisan4060 • updated 2.0 years ago by Rory Stark3.0k
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Using dispersion per gene to run Wald test (DESeq2)
... I am trying to run the DESeq2 with only 1378 genes. This subset of genes are defined by the GO term "DNA binding proteins", as I am only interested in the transcription factors in this data set. I have tried with just the standard workflow of using a common dispersion trend but I think due to the lo ...
deseq2 written 4.0 years ago by meisan4060 • updated 4.0 years ago by Michael Love26k
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Comment: C: DiffBind dba.report to retrieve all sites (differential and non-differential)
... Hi Rory, thanks for helping. The script is working fine now. Mei San ...
written 4.6 years ago by meisan4060
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DiffBind dba.report to retrieve all sites (differential and non-differential)
... This is a question on the dba.report function in DiffBind. I am trying to retrieve all sites (including non-differential and differential sites) by using the following script: GRanges.steady <- dba.report(diff.analysis.steady, method=DBA_DESEQ2_BLOCK, th=1, bUsePval=FALSE) However, the followi ...
diffbind written 4.6 years ago by meisan4060 • updated 4.6 years ago by Rory Stark3.0k
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Comment: C: DiffBind: report only upregulated differential sites
... Hi Rory, Thanks, it helped.  However, I've a couple points for clarification: 1. Could you suggest a way to capture the subset negative and positive fold changes reports as a csv file (equivalent to the "file" parameter in dba.report)? I eventually exported the GRanges object as a bed file using ...
written 5.0 years ago by meisan4060
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DiffBind: report only upregulated differential sites
... This is a question on the dba.report function of DiffBind. I'm trying to retrieve only the upregulated differential sites and have been using the "bUP" and "fold" arguments with the dba.report function, but I've not been able to filter out to obtain only the upregulated differential sites. My R sc ...
diffbind written 5.0 years ago by meisan4060 • updated 5.0 years ago by Rory Stark3.0k
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Comment: C: Technical details of DiffBind correlation analysis
... Hello Rory.   Thanks. Definitely did help. Does the affinity correlation have the same sequence?  I am asking mainly because I have a data set that has very low correlation with the occupancy analysis (~0.2) between replicates, but much higher correlation analysis (~0.8) with the affinity analysi ...
written 5.1 years ago by meisan4060
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Technical details of DiffBind correlation analysis
... I would like to clarify some technical details which I’ve been trying to search for in the documentations for DiffBind, but seem to have missed it. I am interested to know the details of how the correlation of occupancy (using peak caller score) is generated. Is this a Pearson Correlation Coefficien ...
diffbind duplicatecorrelation written 5.1 years ago by meisan4060 • updated 5.1 years ago by Rory Stark3.0k

Latest awards to meisan406

Popular Question 24 months ago, created a question with more than 1,000 views. For DiffBind: report only upregulated differential sites
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Technical details of DiffBind correlation analysis

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