User: niu.shengyong
niu.shengyong • 0
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Posts by niu.shengyong
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... 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 ...
written 2.2 years ago by
niu.shengyong • 0
• updated
2.2 years ago by
Maciej Jończyk • 0
0
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3
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1.4k
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3
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Comment:
C: DiffBind Batch Effect
... Thanks for your help!
...
written 2.2 years ago by
niu.shengyong • 0
0
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3
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1.4k
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3
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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 2.2 years ago by
niu.shengyong • 0
0
votes
3
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1.4k
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3
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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 2.3 years ago by
niu.shengyong • 0
0
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478
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... 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 ...
written 2.3 years ago by
niu.shengyong • 0
• updated
2.3 years ago by
Rory Stark • 2.8k
0
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3
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1.4k
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3
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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 2.3 years ago by
niu.shengyong • 0
0
votes
3
answers
1.4k
views
3
answers
Comment:
C: DiffBind Batch Effect
... Just emailed to you. Thanks!
...
written 2.3 years ago by
niu.shengyong • 0
0
votes
3
answers
1.4k
views
3
answers
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 2.3 years ago by
niu.shengyong • 0
0
votes
3
answers
1.4k
views
3
answers
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 2.3 years ago by
niu.shengyong • 0
0
votes
3
answers
1.4k
views
3
answers
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 2.3 years ago by
niu.shengyong • 0
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