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
