DiffBind reporting error
0
0
Entering edit mode
Ivan • 0
@825f29c7
Last seen 2.9 years 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

DiffBind • 482 views
ADD COMMENT

Login before adding your answer.

Traffic: 733 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6