User: niu.shengyong

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Posts by niu.shengyong

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Homer getDiffExpression.pl issue
... Hi there, I'm now using the function getDiffExpression.pl from Homer with the count table generated from annotatePeaks.pl.   Here is my codes: ​getDiffExpression.pl countTable.peaks.txt ND T2D T2D T2D T2D ND > diffOutput.txt Here is the errors: Argument "-319,filename1..." isn't numeri ...
atac-seq homer written 4 months ago by niu.shengyong0 • updated 4 months ago by Maciej Jończyk0
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Comment: C: DiffBind Batch Effect
... Thanks for your help! ...
written 4 months ago by niu.shengyong0
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Comment: C: DiffBind Batch Effect
... Hi Rory,   Thanks for your help! In this case, how could I evaluate if there is still significant batch effect in my dataset after use the "BLOCK" arguments you mentioned? Thanks! ...
written 5 months ago by niu.shengyong0
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Comment: C: DiffBind Batch Effect
... Thanks Rory! After checking the PCA plot and correlation plot, I find there is still quite significant batch effect. Do you have any advice? Thanks! ...
written 5 months ago by niu.shengyong0
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DiffBind error Error in pv.getPlotData
... I use the following codes to model batch effect for differential analysis from different batches.  ta <- dba(sampleSheet = "diff.csv") ta <- dba.count(ta, summits=75) ta <- dba.contrast(ta, categories=DBA_CONDITION, minMembers = 2,   block=DBA_REPLICATE) ta <- dba.ana ...
diffbind written 5 months ago by niu.shengyong0 • updated 5 months ago by Rory Stark2.1k
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Answer: A: DiffBind Batch Effect
... It works when I tried in another version; however, there is another error now: It shows the following error when I try to plot heatmap or PCA plot. "Error in pv.getPlotData(DBA, attributes = attributes, contrast = contrast,  :  Only one site to plot -- need at least 2!".   Thanks! ...
written 5 months ago by niu.shengyong0
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Comment: C: DiffBind Batch Effect
... Just emailed to you. Thanks! ...
written 5 months ago by niu.shengyong0
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Answer: A: DiffBind Batch Effect
... Hi Rory, I get the message after dba.report: Error in `colnames<-`(`*tmp*`, value = c("Chr", "Start", "End", "Conc", : 'names' attribute [9] must be the same length as the vector [7] I use the version of 2.2.12 and I knew it may be the version issue. Is there any workaround for it if I st ...
written 5 months ago by niu.shengyong0
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Comment: C: DiffBind Batch Effect
... I have 2 batches. One is "batch 3" and another one is "batch 5", so I put numerical value 3 or 5 in the Replicate column.  ...
written 5 months ago by niu.shengyong0
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Comment: C: DiffBind Batch Effect
... Hi Rory, When I follow your suggestions, it shows the error: "Error in pv.DBAreport(pv=DBA, contrast = contrast, method = method: DESeq2 analysis has not been run for this contrast." My codes: ta <- dba(sampleSheet = "diff.csv") ta <- dba.count(ta, summits=75) ta = dba.contrast(ta, categor ...
written 5 months ago by niu.shengyong0

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