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Question: Error in dba.count
0
gravatar for jorrenkuster
5 weeks ago by
jorrenkuster0 wrote:

Dear Sir, Madam,

I run into this problem again and again. I have looked at the same question on Bioconductor before, but for me it still is not working. If someone could please help me, I will be very grateful. 

I am trying to do the dba.count command out of the DiffBind package in R. Creating the dba object works fine for me, but when I wanted to do the counting, this error occurs:

> counts.runx1 <- dba.count(runx1.consensus, readFormat = DBA_READS_BAM, score = DBA_SCORE_READS)
Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,  : 
  Some read files could not be accessed. See warnings for details.
In addition: Warning messages:
1: /Data_ChIP_Experiment/aligned_S00D47H1-RUNX1.filtered.bam not accessible 
2: /Data_ChIP_Experiment/aligned_S00D63H1.filtered.bam not accessible 
3: /Data_ChIP_Experiment/aligned_S00D55H1.filtered.bam not accessible 
4: /Data_ChIP_Experiment/aligned_S00XUNH1-RUNX1.filtered.bam not accessible 
5: /Data_ChIP_Experiment/aligned_SRR1526791.filtered.bam not accessible 
6: /Data_ChIP_Experiment/aligned_SRR772111.filtered.bam not accessible 

Please help me to figure out this problem.

Kind regards, 

Jorren

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DiffBind_1.8.5       GenomicRanges_1.14.4 XVector_0.2.0        IRanges_1.20.7       BiocGenerics_0.8.0  

loaded via a namespace (and not attached):
 [1] amap_0.8-14        bitops_1.0-6       caTools_1.17.1     edgeR_3.4.2        gdata_2.13.3       gplots_2.16.0     
 [7] gtools_3.4.2       KernSmooth_2.23-10 limma_3.18.13      RColorBrewer_1.1-2 stats4_3.0.2       tools_3.0.2       
[13] zlibbioc_1.8.0 

ADD COMMENTlink modified 5 weeks ago by James W. MacDonald43k • written 5 weeks ago by jorrenkuster0
0
gravatar for James W. MacDonald
5 weeks ago by
United States
James W. MacDonald43k wrote:

Your sessionInfo says you are on Windows, but the directories you are specifying are what you would expect on some sort of Linux variant. You have to specify the actual correct location of your files for R to find them.
 

ADD COMMENTlink written 5 weeks ago by James W. MacDonald43k
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