During dba(sampleSheet = "samples.csv") step, Error in mergeScores(merged, def, peakset, TRUE) : Not compatible with requested type: [type=character; target=double].
Entering edit mode
niimabear • 0
Last seen 19 months ago

New to R, but enthusiastic to start easing into the world of bioinformatics analysis. Currently partway through my PhD, creating and testing new protocols (ChIP-Seq, bioinformatics analyses) solo in a small research group without an expert or experienced Post-Doc/PI to provide guidance.

I've read through the DiffBind Vignette a few dozen times, and followed through a video tutorial hosted on the Cancer Research UK site a half dozen more, worked through dozens of pretty niave error codes to get here. I'm still learning so thanks for your patients.

I keep running into this error code now that I've walked through using DiffBind in R Studio with a practise sample sheet (with only a few samples versus all my samples for ease of use and ease of troubleshooting). Example samplesheet run did not have this problem.

With my full sample sheet created and read into RStudio, I keep getting the following error right at the beginning of the analysis.

Troubleshooting so far has included:

  • checking paths in R to confirm files exist and haven't been pulled into iCloud (using mac laptop).
  • checking all .bam files have data/aren't empty, everything seems to be fine.
  • checking that R is up to date, and current version of Bioconductor/BiocManager/DiffBind are being used.

In my limited experience, I can't conceptualize what's going wrong. To the best of my investigative skills, the information on BioStars or this Bioconductor Help site have been limited related to this specific error code.

Thanks in advance for time and help!

```samples <-dba(sampleSheet = "SampleSheetPreIPs2.csv") WTMxP_1 homzygote MxP 1 macs WTMdP_1 homzygote MdP 1 macs WTPA2_1 homzygote PA2 1 macs HetMdP_1 heterozygote MdP 1 macs WTMxP_2 homzygote MxP 2 macs WTMdP_2 homzygote MdP 2 macs WTPA2_2 homzygote PA2 2 macs HetMxP_2 heterozygote MxP 2 macs HetPA2_2 heterozygote PA2 2 macs WTMdP_3 homzygote MdP 3 macs WTPA2_3 homzygote PA2 3 macs HetMxP_3 heterozygote MxP 3 macs HetMdP_3 heterozygote MdP 3 macs HetPA2_3 heterozygote PA2 3 macs Error in mergeScores(merged, def, peakset, TRUE) : Not compatible with requested type: [type=character; target=double].

sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.4

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages: [1] DESeq2_1.36.0 DiffBind_3.6.1 SummarizedExperiment_1.26.1 Biobase_2.56.0 MatrixGenerics_1.8.1
[6] matrixStats_0.62.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 IRanges_2.30.0 S4Vectors_0.34.0
[11] BiocGenerics_0.42.0 BiocManager_1.30.18

loaded via a namespace (and not attached): [1] bitops_1.0-7 bit64_4.0.5 httr_1.4.3 RColorBrewer_1.1-3 numDeriv_2016.8-1.1
[6] tools_4.2.0 utf8_1.2.2 R6_2.5.1 irlba_2.3.5 KernSmooth_2.23-20
[11] DBI_1.1.3 colorspace_2.0-3 apeglm_1.18.0 tidyselect_1.1.2 bit_4.0.4
[16] compiler_4.2.0 cli_3.3.0 DelayedArray_0.22.0 rtracklayer_1.56.1 caTools_1.18.2
[21] scales_1.2.0 SQUAREM_2021.1 mvtnorm_1.1-3 genefilter_1.78.0 mixsqp_0.3-43
[26] stringr_1.4.0 digest_0.6.29 Rsamtools_2.12.0 XVector_0.36.0 jpeg_0.1-9
[31] pkgconfig_2.0.3 htmltools_0.5.2 fastmap_1.1.0 invgamma_1.1 bbmle_1.0.25
[36] limma_3.52.2 BSgenome_1.64.0 htmlwidgets_1.5.4 rlang_1.0.3 RSQLite_2.2.14
[41] BiocIO_1.6.0 generics_0.1.2 hwriter_1.3.2.1 BiocParallel_1.30.3 gtools_3.9.2.2
[46] dplyr_1.0.9 RCurl_1.98-1.7 magrittr_2.0.3 GenomeInfoDbData_1.2.8 Matrix_1.4-1
[51] Rcpp_1.0.8.3 munsell_0.5.0 fansi_1.0.3 lifecycle_1.0.1 stringi_1.7.6
[56] yaml_2.3.5 MASS_7.3-57 zlibbioc_1.42.0 gplots_3.1.3 plyr_1.8.7
[61] blob_1.2.3 grid_4.2.0 parallel_4.2.0 ggrepel_0.9.1 bdsmatrix_1.3-6
[66] crayon_1.5.1 lattice_0.20-45 splines_4.2.0 Biostrings_2.64.0 annotate_1.74.0
[71] KEGGREST_1.36.2 locfit_1.5-9.5 pillar_1.7.0 rjson_0.2.21 systemPipeR_2.2.2
[76] geneplotter_1.74.0 codetools_0.2-18 XML_3.99-0.10 glue_1.6.2 ShortRead_1.54.0
[81] GreyListChIP_1.28.1 latticeExtra_0.6-29 png_0.1-7 vctrs_0.4.1 gtable_0.3.0
[86] purrr_0.3.4 amap_0.8-18 cachem_1.0.6 ashr_2.2-54 ggplot2_3.3.6
[91] emdbook_1.3.12 xtable_1.8-4 restfulr_0.0.15 coda_0.19-4 survival_3.3-1
[96] truncnorm_1.0-8 tibble_3.1.7 memoise_2.0.1 AnnotationDbi_1.58.0 GenomicAlignments_1.32.0 [101] ellipsis_0.3.2

DiffBind • 1.0k views
Entering edit mode

I see the PeakCaller is set to macs, are your peak files the .xls files generated by MACS?

If they are, it would help to see your sample sheet and at least one (preferably all) of the peak files (you can email to me if you want).


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