Entering edit mode
7.2 years ago
zhaolin20042008
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10
Hello, I have been working with DiffBind for 6 months. Recently I got some warnings when I update DiffBind 2.6.1. Then previously worked scripts failed to run in DiffBind 2.6.1. I reinstalled the older version 2.4.8 again,however, dba.count still failed if I chose score=DBA_SCORE_SUMMIT but works if I chose score=DBA_SCORE_RPKM. Since the data from ATAC-seq, I was told score=DBA_SCORE_SUMMIT is recommended. Could anyone help me with the problem? Thanks a lot.
Warning messages:
1: no function found corresponding to methods exports from âDelayedArrayâ for: âacbindâ, âarbindâ
2: no function found corresponding to methods exports from âSummarizedExperimentâ for: âacbindâ, âarbindâ
3: multiple methods tables found for ârglistâ
4: multiple methods tables found for âOntologyâ
5: replacing previous import âAnnotationDbi::Ontologyâ by âBiocGenerics::Ontologyâ when loading âGenomicFeaturesâ
6: In .recacheSubclasses(def@className, def, doSubclasses, ... :
undefined subclass "GIntervalTree" of class "GenomicRangesORGenomicRangesList"; definition not updated
7: In .recacheSubclasses(def@className, def, doSubclasses, ... :
undefined subclass "GIntervalTree" of class "RangedDataORGenomicRanges"; definition not updated
8: In .recacheSubclasses(def@className, def, doSubclasses, ... :
undefined subclass "RangedDataList" of class "RangedDataORRangedDataList"; definition not updated
9: multiple methods tables found for âspaceâ
10: replacing previous import âBiocGenerics::Ontologyâ by âAnnotationDbi::Ontologyâ when loading âannotateâ
11: multiple methods tables found for âOntologyâ
12: replacing previous import âBiocGenerics::Ontologyâ by âAnnotationDbi::Ontologyâ when loading âAnnotationForgeâ
Error Information
> eiff<-dba.count(eiff, minOverlap=12,score=DBA_SCORE_SUMMIT,summits=150,readFormat=DBA_READS_DEFAULT, bParallel=eiff$config$RunParallel)
Re-centering peaks...
Error in heights * sapply(called, function(x) x) : non-conformable arrays
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] DiffBind_2.6.1 SummarizedExperiment_1.6.5
[3] DelayedArray_0.2.7 matrixStats_0.52.2
[5] Biobase_2.36.2 GenomicRanges_1.30.0
[7] GenomeInfoDb_1.14.0 IRanges_2.12.0
[9] S4Vectors_0.16.0 BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] edgeR_3.18.1 bit64_0.9-7 splines_3.4.2
[4] gtools_3.5.0 assertthat_0.2.0 latticeExtra_0.6-28
[7] amap_0.8-14 RBGL_1.52.0 blob_1.1.0
[10] GenomeInfoDbData_0.99.0 Rsamtools_1.28.0 ggrepel_0.7.0
[13] Category_2.42.1 RSQLite_2.0 backports_1.1.1
[16] lattice_0.20-35 glue_1.2.0 limma_3.32.7
[19] digest_0.6.12 RColorBrewer_1.1-2 XVector_0.16.0
[22] checkmate_1.8.5 colorspace_1.3-2 Matrix_1.2-12
[25] plyr_1.8.4 GSEABase_1.38.2 XML_3.98-1.9
[28] pkgconfig_2.0.1 pheatmap_1.0.8 ShortRead_1.34.1
[31] biomaRt_2.32.1 genefilter_1.58.1 zlibbioc_1.22.0
[34] xtable_1.8-2 GO.db_3.4.1 scales_0.5.0
[37] brew_1.0-6 gdata_2.18.0 BiocParallel_1.10.1
[40] tibble_1.3.4 annotate_1.54.0 ggplot2_2.2.1
[43] GenomicFeatures_1.28.5 lazyeval_0.2.0 magrittr_1.5
[46] survival_2.41-3 memoise_1.1.0 systemPipeR_1.10.2
[49] fail_1.3 gplots_3.0.1 hwriter_1.3.2
[52] GOstats_2.42.0 graph_1.54.0 tools_3.4.2
[55] BBmisc_1.11 stringr_1.2.0 sendmailR_1.2-1
[58] munsell_0.4.3 locfit_1.5-9.1 bindrcpp_0.2
[61] AnnotationDbi_1.38.2 Biostrings_2.44.2 compiler_3.4.2
[64] caTools_1.17.1 rlang_0.1.4 grid_3.4.2
[67] RCurl_1.95-4.8 rjson_0.2.15 AnnotationForge_1.18.2
[70] bitops_1.0-6 base64enc_0.1-3 gtable_0.2.0
[73] DBI_0.7 R6_2.2.2 GenomicAlignments_1.12.2
[76] dplyr_0.7.4 rtracklayer_1.30.4 bit_1.1-12
[79] bindr_0.1 KernSmooth_2.23-15 stringi_1.1.5
[82] BatchJobs_1.6 Rcpp_0.12.13
You'd likely get a quicker response by posting on the Bioconductor forum. The authors are pretty active there.
Thanks for suggestion. I will try.