Question: Diffbind: an error when generating DBA lies
0
gravatar for zdong
9 months ago by
zdong20
zdong20 wrote:

Hi

I analyzed the differential binding of the Chip-Seq results. There is an error when generating the dab file using bdobj=dba(sampleSheet = "Bcell.csv"):
the error is like the following:

1 B_cell mRH   1 bed
Error in if file.info(peaks)$size > 0) { : 
  missing value where TRUE/FALSE needed"

Does anyone have any suggestions? The script is the following:

Bnarrow=read.csv("Bcell.csv")
Bnarrow
  Sample.ID Tissue Factor Condition Treatment Replicate              bamReads  Control.ID                bamControl
1      wt1B B_cell    mRH        NA        NA         1  /Diffbind/wt1_RH.bam  wt1_MNctrl  /Diffbind/wt1_MNctrl.bam
2      wt2B B_cell    mRH        NA        NA         2  /Diffbind/wt2_RH.bam  wt2_MNctrl  /Diffbind/wt2_MNctrl.bam
3     dko1B B_cell    mRH        NA        NA         1 /Diffbind/dko1_RH.bam dko1_MNctrl /Diffbind/dko1_MNctrl.bam
4     dko1B B_cell    mRH        NA        NA         2 /Diffbind/dko2_RH.bam dko2_MNctrl /Diffbind/dko2_MNctrl.bam
                                 Peaks PeakCaller
1  /Diffbind/wt1_Bcell_narrowPeaks.bed        bed
2  /Diffbind/wt2_Bcell_narrowPeaks.bed        bed
3 /Diffbind/dko1_Bcell_narrowPeaks.bed        bed
4  /Diffbind/dko2_BcellnarrowPeaks.bed        bed
> bdobj=dba(sampleSheet = "Bcell.csv")
1 B_cell mRH   1 bed
Error in if file.info(peaks)$size > 0) { : 
  missing value where TRUE/FALSE needed
chip-seq • 927 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by zdong20

did you ever figure out the problem? I am currently getting the same error....

ADD REPLYlink written 24 days ago by srmccutcheon0
2
gravatar for zdong
9 months ago by
zdong20
zdong20 wrote:

I have solved the problem, the name of bed file is not correct, and the location of all bam and bed files must exactly correct.

ADD COMMENTlink written 9 months ago by zdong20

Thanks for posting about file location not correct. That's helpful!

ADD REPLYlink written 7 months ago by olechnwin30
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