Hi I was trying to use DiffBind to analysis my ChIP-seq data.

Following the sample given by Vignette, I created my sample sheet ("my_samples_sheet.csv")like this: 

"SampleID","Tissue","Factor","Condition","Treatment","Replicate","bamReads","ControlID","bamControl","Peaks","PeakCaller"
"H3K27ac_XcKOCA","CA","H3K27ac","XcKO","ex_vivo","1","H3K27ac_XcKOCA.bam","Uni_Input","H3K27ac_Input.bam","H3K27acCA_peaks_Enhancers_withSuper.bed","bed"
"H3K27ac_XcKOCB","CB","H3K27ac","XcKO","ex_vivo","1","H3K27ac_XcKOCB.bam","Uni_Input","H3K27ac_Input.bam","H3K27acCB_peaks_Enhancers_withSuper.bed","bed"
"H3K27ac_XcKOCC","CC","H3K27ac","XcKO","ex_vivo","1","H3K27ac_XcKOCellC.bam","Uni_Input","H3K27ac_Input.bam","H3K27acCC_peaks_Enhancers_withSuper.bed","bed"
"H3K27ac_WTCB","CB","H3K27ac","WT","ex_vivo","1","H3K27ac_WTCB.bam","Uni_Input","H3K27ac_Input.bam","H3K27acCB_peaks_Enhancers_withSuper.bed","bed"
"H3K27ac_WTCC","CC","H3K27ac","WT","ex_vivo","1","H3K27ac_WTCC.bam","Uni_Input","H3K27ac_Input.bam","H3K27acCC_peaks_Enhancers_withSuper.bed","bed"
"H3K27ac_WTCA","CA","H3K27ac","WT","ex_vivo","1","H3K27ac_WTCA.bam","Uni_Input","H3K27ac_Input.bam","H3K27acCA_peaks_Enhancers_withSuper.bed","bed"


> sampleTable <- read.csv("my_samples_sheet.csv")
> sampleTable
             SampleID Tissue  Factor Condition Treatment Replicate
1      H3K27ac_XcKOCA    CA  H3K27ac      XcKO   ex_vivo         1
2      H3K27ac_XcKOCB    CB  H3K27ac      XcKO   ex_vivo         1
3      H3K27ac_XcKOCC    CC  H3K27ac      XcKO   ex_vivo         1
4        H3K27ac_WTCB    CB  H3K27ac        WT   ex_vivo         1
5        H3K27ac_WTCC    CC  H3K27ac        WT   ex_vivo         1
6        H3K27ac_WTCA    CA  H3K27ac        WT   ex_vivo         1
                 bamReads ControlID        bamControl
1      H3K27ac_XcKOCA.bam Uni_Input H3K27ac_Input.bam
2      H3K27ac_XcKOCB.bam Uni_Input H3K27ac_Input.bam
3      H3K27ac_XcKOCC.bam Uni_Input H3K27ac_Input.bam
4        H3K27ac_WTCB.bam Uni_Input H3K27ac_Input.bam
5        H3K27ac_WTCC.bam Uni_Input H3K27ac_Input.bam
6        H3K27ac_WTCA.bam Uni_Input H3K27ac_Input.bam
                                       Peaks PeakCaller
1    H3K27acCA_peaks_Enhancers_withSuper.bed        bed
2    H3K27acCB_peaks_Enhancers_withSuper.bed        bed
3    H3K27acCC_peaks_Enhancers_withSuper.bed        bed
4    H3K27acCB_peaks_Enhancers_withSuper.bed        bed
5    H3K27acCC_peaks_Enhancers_withSuper.bed        bed
6    H3K27acCA_peaks_Enhancers_withSuper.bed        bed

but when I tried to read peaksets:

H3K27ac <- dba(sampleSheet="my_samples_sheet.csv",)

I had error like this: 

H3K27ac_XcKOCA CA H3K27ac XcKO ex_vivo 1 bed
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : 
line 2 did not have 23 elements.​

Could anyone let me know what went wrong? Thanks in advance!

PS: 

> sessionInfo()

R version 3.2.3 (2015-12-10)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)


locale:

 [1] LC_CTYPE=ja_JP.UTF-8       LC_NUMERIC=C              

 [3] LC_TIME=ja_JP.UTF-8        LC_COLLATE=ja_JP.UTF-8    

 [5] LC_MONETARY=ja_JP.UTF-8    LC_MESSAGES=ja_JP.UTF-8   

 [7] LC_PAPER=ja_JP.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=ja_JP.UTF-8 LC_IDENTIFICATION=C       


attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets 

[8] methods   base     


other attached packages:

 [1] DiffBind_1.16.3            RSQLite_1.1-2             

 [3] locfit_1.5-9.1             GenomicAlignments_1.6.3   

 [5] Rsamtools_1.22.0           Biostrings_2.38.4         

 [7] XVector_0.10.0             limma_3.26.9              

 [9] SummarizedExperiment_1.0.2 Biobase_2.30.0            

[11] GenomicRanges_1.22.4       GenomeInfoDb_1.6.3        

[13] IRanges_2.4.8              S4Vectors_0.8.11          

[15] BiocGenerics_0.16.1       


loaded via a namespace (and not attached):

 [1] Rcpp_0.12.9             lattice_0.20-33         GO.db_3.2.2            

 [4] gtools_3.5.0            assertthat_0.1          digest_0.6.12          

 [7] plyr_1.8.4              backports_1.0.5         futile.options_1.0.0   

[10] BatchJobs_1.6           ShortRead_1.28.0        ggplot2_2.2.1          

[13] gplots_3.0.1            zlibbioc_1.16.0         GenomicFeatures_1.22.13

[16] lazyeval_0.2.0          annotate_1.48.0         gdata_2.17.0           

[19] Matrix_1.2-8            checkmate_1.8.2         systemPipeR_1.4.8      

[22] GOstats_2.36.0          splines_3.2.3           BiocParallel_1.4.3     

[25] stringr_1.1.0           pheatmap_1.0.8          RCurl_1.95-4.8         

[28] biomaRt_2.26.1          munsell_0.4.3           sendmailR_1.2-1        

[31] rtracklayer_1.30.4      base64enc_0.1-3         BBmisc_1.10            

[34] fail_1.3                tibble_1.2              edgeR_3.12.1           

[37] XML_3.98-1.5            AnnotationForge_1.12.2  bitops_1.0-6           

[40] grid_3.2.3              RBGL_1.46.0             xtable_1.8-2           

[43] GSEABase_1.32.0         gtable_0.2.0            DBI_0.5-1              

[46] magrittr_1.5            scales_0.4.1            graph_1.48.0           

[49] KernSmooth_2.23-15      amap_0.8-14             stringi_1.1.2          

[52] hwriter_1.3.2           genefilter_1.52.1       latticeExtra_0.6-28    

[55] futile.logger_1.4.3     brew_1.0-6              rjson_0.2.15           

[58] lambda.r_1.1.9          RColorBrewer_1.1-2      tools_3.2.3            

[61] Category_2.36.0         survival_2.40-1         AnnotationDbi_1.32.3   

[64] colorspace_1.3-2        caTools_1.17.1          memoise_1.0.0 

It would help to see the first two lines of the file H3K27acCA_peaks_Enhancers_withSuper.bed. I suspect that trimming the first line would help.

Also, I see you are running a very old version of DiffBind (v1.16.3), you may want to update to a more recent version.

Regards-

Rory