Question: Error in dba.count
gravatar for jorrenkuster
14 months 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, 


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

[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 14 months ago by James W. MacDonald46k • written 14 months ago by jorrenkuster0
gravatar for James W. MacDonald
14 months ago by
United States
James W. MacDonald46k 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 14 months ago by James W. MacDonald46k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 122 users visited in the last hour