DiffBind reporting error
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Ivan • 0
@825f29c7
Last seen 4 months ago
Italy

Hi, I have a problem with dba.report, which gives the error below. This is limited to edger, while it works fine with DESeq2. Any idea of why? Ivan

# edgeR
dbind.report.edger <- dba.report(DBA = dbind_de, contrast = 1, method = DBA_EDGER, th = fdr_thr, fold = lfc_thr)

Error in .Call2("C_solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : In range 1222: at least two out of 'start', 'end', and 'width', must be supplied.

# DESeq2
dbind.report.deseq2 <- dba.report(DBA = dbind_de, contrast = 1, method = DBA_DESEQ2, th = fdr_thr, fold = lfc_thr)

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /opt/common/tools/ric.tiget/anaconda3/envs/atac/lib/libopenblasp-r0.3.12.so

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] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] openxlsx_4.2.3 DiffBind_3.0.13 SummarizedExperiment_1.20.0 Biobase_2.50.0
[5] MatrixGenerics_1.2.1 matrixStats_0.58.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.2
[9] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.0

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