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Hello! I am currently using DiffBind 3.6.1 and encountering the following error when attempting to analyze my data:
> dba <- dba.contrast(dba, design = "~Condition")
Computing results names...
> dba <- dba.analyze(dba)
Applying Blacklist/Greylists...
Genome detected: Hsapiens.UCSC.hg38
Applying blacklist...
Removed: 276 of 43183 intervals.
Counting control reads for greylist...
Blacklist error: Error in value[[3L]](cond): GreyListChIP error: Error: $ operator is invalid for atomic vectors
Unable to apply Blacklist/Greylist.
Do you know what might be the issue?
Here is my sessionInfo()
:
> sessionInfo()
R version 4.2.0 (2022-04-22)
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_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] RLSeq_1.2.0 DiffBind_3.6.1 SummarizedExperiment_1.26.1 Biobase_2.56.0
[5] MatrixGenerics_1.8.0 matrixStats_0.62.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.1
[9] IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0 forcats_0.5.1
[13] stringr_1.4.0 dplyr_1.0.9 purrr_0.3.4 readr_2.1.2
[17] tidyr_1.2.0 tibble_3.1.7 ggplot2_3.3.6 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] utf8_1.2.2 tidyselect_1.1.2 RSQLite_2.2.14 AnnotationDbi_1.58.0
[5] htmlwidgets_1.5.4 grid_4.2.0 BiocParallel_1.30.3 aws.signature_0.6.0
[9] pROC_1.18.0 munsell_0.5.0 codetools_0.2-18 systemPipeR_2.2.2
[13] future_1.25.0 withr_2.5.0 colorspace_2.0-3 filelock_1.0.2
[17] rstudioapi_0.13 listenv_0.8.0 bbmle_1.0.25 GenomeInfoDbData_1.2.8
[21] mixsqp_0.3-43 hwriter_1.3.2.1 bit64_4.0.5 coda_0.19-4
[25] parallelly_1.31.1 vctrs_0.4.1 generics_0.1.2 ipred_0.9-12
[29] BiocFileCache_2.4.0 regioneR_1.28.0 R6_2.5.1 apeglm_1.18.0
[33] invgamma_1.1 locfit_1.5-9.5 bitops_1.0-7 cachem_1.0.6
[37] DelayedArray_0.22.0 assertthat_0.2.1 vroom_1.5.7 promises_1.2.0.1
[41] BiocIO_1.6.0 scales_1.2.0 nnet_7.3-17 gtable_0.3.0
[45] valr_0.6.4 globals_0.15.0 processx_3.5.3 timeDate_3043.102
[49] rlang_1.0.2 genefilter_1.78.0 splines_4.2.0 rtracklayer_1.56.0
[53] ModelMetrics_1.2.2.2 broom_0.8.0 RLHub_1.2.0 BiocManager_1.30.17
[57] yaml_2.3.5 reshape2_1.4.4 modelr_0.1.8 GenomicFeatures_1.48.0
[61] backports_1.4.1 httpuv_1.6.5 caret_6.0-92 tools_4.2.0
[65] lava_1.6.10 ellipsis_0.3.2 gplots_3.1.3 RColorBrewer_1.1-3
[69] Rcpp_1.0.8.3 plyr_1.8.7 base64enc_0.1-3 progress_1.2.2
[73] zlibbioc_1.42.0 RCurl_1.98-1.6 ps_1.7.0 prettyunits_1.1.1
[77] rpart_4.1.16 pbapply_1.5-0 ashr_2.2-54 haven_2.5.0
[81] ggrepel_0.9.1 fs_1.5.2 magrittr_2.0.3 data.table_1.14.2
[85] caretEnsemble_2.0.1 reprex_2.0.1 truncnorm_1.0-8 mvtnorm_1.1-3
[89] SQUAREM_2021.1 amap_0.8-18 hms_1.1.1 mime_0.12
[93] xtable_1.8-4 XML_3.99-0.9 emdbook_1.3.12 jpeg_0.1-9
[97] readxl_1.4.0 gridExtra_2.3 compiler_4.2.0 biomaRt_2.52.0
[101] bdsmatrix_1.3-4 KernSmooth_2.23-20 crayon_1.5.1 htmltools_0.5.2
[105] later_1.3.0 tzdb_0.3.0 geneplotter_1.74.0 aws.s3_0.3.21
[109] lubridate_1.8.0 DBI_1.1.2 ExperimentHub_2.4.0 dbplyr_2.1.1
[113] MASS_7.3-57 rappdirs_0.3.3 ShortRead_1.54.0 Matrix_1.4-1
[117] cli_3.3.0 parallel_4.2.0 gower_1.0.0 pkgconfig_2.0.3
[121] GenomicAlignments_1.32.0 numDeriv_2016.8-1.1 recipes_0.2.0 xml2_1.3.3
[125] foreach_1.5.2 annotate_1.74.0 hardhat_0.2.0 XVector_0.36.0
[129] prodlim_2019.11.13 rvest_1.0.2 callr_3.7.0 digest_0.6.29
[133] Biostrings_2.64.0 cellranger_1.1.0 restfulr_0.0.13 GreyListChIP_1.28.0
[137] curl_4.3.2 shiny_1.7.1 Rsamtools_2.12.0 gtools_3.9.2
[141] rjson_0.2.21 lifecycle_1.0.1 nlme_3.1-157 jsonlite_1.8.0
[145] limma_3.52.0 BSgenome_1.64.0 fansi_1.0.3 pillar_1.7.0
[149] lattice_0.20-45 KEGGREST_1.36.0 fastmap_1.1.0 httr_1.4.3
[153] survival_3.2-13 interactiveDisplayBase_1.34.0 glue_1.6.2 png_0.1-7
[157] iterators_1.0.14 BiocVersion_3.15.2 bit_4.0.4 class_7.3-20
[161] stringi_1.7.6 blob_1.2.3 DESeq2_1.36.0 AnnotationHub_3.4.0
[165] latticeExtra_0.6-29 caTools_1.18.2 memoise_2.0.1 irlba_2.3.5
[169] future.apply_1.9.0
I would welcome the opportunity to debug this issue if you were willing to send me your DBA object
dba
and a link to a place I could access the control reads.In the meantime, you can turn off greylist generation by either setting
bGreylist=FALSE
when callingdba.analyze()
or setting