DiffBind does not load samples
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nw416 • 0
@c90736ae
Last seen 9 months ago
United Kingdom

I am trying to analyse a ChIP-Seq data set with DiffBind. These are the contents of my sample sheet ("diffbind_samples.csv"):

SampleID,Tissue,Factor,Condition,Treatment,Replicate,bamReads,ControlID,bamControl,Peaks,PeakCaller
HC,Neutrophils,H3K4me3,HC,Ex-vivo,1,bam/merged/HC_H3K4me3.bam,HC_input,bam/merged/HC_H3K4me3_input.bam,peak/H3K4me3-healthy_control_peaks.xls,macs
ARNT,Neutrophils,H3K4me3,ARNT,Ex-vivo,1,bam/merged/ARNTHC_H3K4me3.bam,ARNT_input,bam/merged/ARNTHC_H3K4me3_input.bam,peak/H3K4me3-ARNT_peaks.xls,macs
ARDT,Neutrophils,H3K4me3,ARDT,Ex-vivo,1,bam/merged/ARDTHC_H3K4me3.bam,ARDT_input,bam/merged/ARDTHC_H3K4me3_input.bam,peak/H3K4me3-ARDT_peaks.xls,macs

When I run dba.analyze("diffbind_samples.csv"), I get this error:

Loading sample sheet...
HC Neutrophils H3K4me3 Healthy_control Ex_vivo 1 macs
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 1 did not have 4 elements

It suggests it has something to do with the sample sheet, but I really can't find what it is wrong with it. To generate this sample sheet, I took the tamoxifen.csv file from the demo data set and replaced all the values with my own. Does anyone see what I am doing wrong? I have been stuck at this step for days now. It must be something really obvious that I am not seeing.

Output of sessionInfo():

R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] DiffBind_3.2.7              SummarizedExperiment_1.22.0
 [3] Biobase_2.52.0              MatrixGenerics_1.4.3       
 [5] matrixStats_0.61.0          GenomicRanges_1.44.0       
 [7] GenomeInfoDb_1.28.4         IRanges_2.26.0             
 [9] S4Vectors_0.30.2            BiocGenerics_0.38.0        

loaded via a namespace (and not attached):
  [1] backports_1.4.1          GOstats_2.58.0           BiocFileCache_2.0.0     
  [4] plyr_1.8.7               GSEABase_1.54.0          splines_4.1.3           
  [7] BiocParallel_1.26.2      ggplot2_3.3.5            amap_0.8-18             
 [10] digest_0.6.29            invgamma_1.1             GO.db_3.13.0            
 [13] SQUAREM_2021.1           fansi_1.0.3              magrittr_2.0.2          
 [16] checkmate_2.0.0          memoise_2.0.1            BSgenome_1.60.0         
 [19] base64url_1.4            limma_3.48.3             Biostrings_2.60.2       
 [22] annotate_1.70.0          systemPipeR_1.26.3       bdsmatrix_1.3-4         
 [25] prettyunits_1.1.1        jpeg_0.1-9               colorspace_2.0-3        
 [28] blob_1.2.2               rappdirs_0.3.3           apeglm_1.14.0           
 [31] ggrepel_0.9.1            dplyr_1.0.8              crayon_1.5.1            
 [34] RCurl_1.98-1.6           jsonlite_1.8.0           graph_1.70.0            
 [37] genefilter_1.74.1        brew_1.0-7               survival_3.2-13         
 [40] VariantAnnotation_1.38.0 glue_1.6.2               gtable_0.3.0            
 [43] zlibbioc_1.38.0          XVector_0.32.0           DelayedArray_0.18.0     
 [46] V8_4.1.0                 Rgraphviz_2.36.0         scales_1.1.1            
 [49] pheatmap_1.0.12          mvtnorm_1.1-3            DBI_1.1.2               
 [52] edgeR_3.34.1             Rcpp_1.0.8.3             xtable_1.8-4            
 [55] progress_1.2.2           emdbook_1.3.12           bit_4.0.4               
 [58] rsvg_2.2.0               AnnotationForge_1.34.1   truncnorm_1.0-8         
 [61] httr_1.4.2               gplots_3.1.1             RColorBrewer_1.1-2      
 [64] ellipsis_0.3.2           pkgconfig_2.0.3          XML_3.99-0.9            
 [67] dbplyr_2.1.1             locfit_1.5-9.5           utf8_1.2.2              
 [70] tidyselect_1.1.2         rlang_1.0.2              AnnotationDbi_1.54.1    
 [73] munsell_0.5.0            tools_4.1.3              cachem_1.0.6            
 [76] cli_3.2.0                generics_0.1.2           RSQLite_2.2.11          
 [79] stringr_1.4.0            fastmap_1.1.0            yaml_2.3.5              
 [82] bit64_4.0.5              caTools_1.18.2           purrr_0.3.4             
 [85] KEGGREST_1.32.0          RBGL_1.68.0              xml2_1.3.3              
 [88] biomaRt_2.48.3           compiler_4.1.3           filelock_1.0.2          
 [91] curl_4.3.2               png_0.1-7                geneplotter_1.70.0      
 [94] tibble_3.1.6             stringi_1.7.6            GenomicFeatures_1.44.2  
 [97] lattice_0.20-45          Matrix_1.4-0             vctrs_0.3.8             
[100] pillar_1.7.0             lifecycle_1.0.1          data.table_1.14.2       
[103] bitops_1.0-7             irlba_2.3.5              rtracklayer_1.52.1      
[106] R6_2.5.1                 BiocIO_1.2.0             latticeExtra_0.6-29     
[109] hwriter_1.3.2            ShortRead_1.50.0         KernSmooth_2.23-20      
[112] MASS_7.3-56              gtools_3.9.2             assertthat_0.2.1        
[115] DESeq2_1.32.0            Category_2.58.0          rjson_0.2.21            
[118] withr_2.5.0              GenomicAlignments_1.28.0 batchtools_0.9.15       
[121] Rsamtools_2.8.0          GenomeInfoDbData_1.2.6   hms_1.1.1               
[124] grid_4.1.3               DOT_0.1                  coda_0.19-4             
[127] GreyListChIP_1.24.0      ashr_2.2-54              mixsqp_0.3-43           
[130] bbmle_1.0.24             numDeriv_2016.8-1.1      restfulr_0.0.13
DiffBind • 615 views
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