Entering edit mode
2.2 years ago
justinian458
•
0
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
1 HC Neutrophils H3K4me3 Healthy_control Ex_vivo 1
2 ARNT Neutrophils H3K4me3 ARNT Ex_vivo 1
3 ARDT Neutrophils H3K4me3 ARDT Ex_vivo 1
bamReads ControlID bamControl
1 bam/merged/HC_H3K4me3.bam HC_input bam/merged/HC_H3K4me3_input.bam
2 bam/merged/ARNTHC_H3K4me3.bam ARNT_input bam/merged/ARNTHC_H3K4me3_input.bam
3 bam/merged/ARDTHC_H3K4me3.bam ARDT_input bam/merged/ARDTHC_H3K4me3_input.bam
Peaks PeakCaller
1 peak/H3K4me3-healthy_control_peaks.xls macs
2 peak/H3K4me3-ARDT_peaks.xls macs
3 peak/H3K4me3-ARDT_peaks.xls macs
When I run dba.analyze("diffbind_samples.csv"), I get this error:
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. When I compare it do the demo sample sheet it looks similar. Does anyone see what I am doing wrong? Thank you.
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
