Parameter bSubControl with no effect in dba.count?

Question

[frueher]

Dear all, I am using DiffBind for ChIP-Seq and CUTnTag analysis and would like to switch off subtracting reads of control samples. For this, I set bSubControl=FALSE in dba.count(). However, DiffBind results are exactly identical no matter if I set bSubControl to TRUE or FALSE. I tried this for several R and DiffBind versions with R v4.3.2 and DiffBind_3.10.1 being the latest, but it was the same for all of them. Anyone else having the same problem?

Here is my sessionInfo():

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
 [1] ggplot2_3.4.3               dplyr_1.1.3
 [3] openxlsx_4.2.5.2            DiffBind_3.10.1
 [5] SummarizedExperiment_1.30.2 Biobase_2.60.0
 [7] MatrixGenerics_1.12.3       matrixStats_1.0.0
 [9] GenomicRanges_1.52.0        GenomeInfoDb_1.36.3
[11] IRanges_2.34.1              S4Vectors_0.38.1
[13] BiocGenerics_0.46.0

loaded via a namespace (and not attached):
 [1] bitops_1.0-7             deldir_1.0-9             rlang_1.1.1
 [4] magrittr_2.0.3           compiler_4.3.2           png_0.1-8
 [7] systemfonts_1.0.5        vctrs_0.6.3              stringr_1.5.0
[10] pkgconfig_2.0.3          crayon_1.5.2             fastmap_1.1.1
[13] XVector_0.40.0           labeling_0.4.3           caTools_1.18.2
[16] utf8_1.2.4               Rsamtools_2.16.0         ragg_1.2.6
[19] zlibbioc_1.46.0          DelayedArray_0.26.7      BiocParallel_1.34.2
[22] jpeg_0.1-10              irlba_2.3.5.1            R6_2.5.1
[25] stringi_1.7.12           RColorBrewer_1.1-3       SQUAREM_2021.1
[28] limma_3.56.2             rtracklayer_1.60.1       numDeriv_2016.8-1.1
[31] Rcpp_1.0.11              Matrix_1.6-4             tidyselect_1.2.0
[34] abind_1.4-5              yaml_2.3.7               gplots_3.1.3
[37] codetools_0.2-19         hwriter_1.3.2.1          lattice_0.22-5
[40] tibble_3.2.1             plyr_1.8.8               withr_2.5.1
[43] ShortRead_1.58.0         csaw_1.34.0              coda_0.19-4
[46] zip_2.3.0                Biostrings_2.68.1        pillar_1.9.0
[49] KernSmooth_2.23-22       generics_0.1.3           invgamma_1.1
[52] RCurl_1.98-1.12          truncnorm_1.0-9          emdbook_1.3.13
[55] munsell_0.5.0            scales_1.2.1             ashr_2.2-63
[58] gtools_3.9.4             glue_1.6.2               metapod_1.8.0
[61] tools_4.3.2              apeglm_1.22.1            interp_1.1-4
[64] BiocIO_1.10.0            BSgenome_1.68.0          locfit_1.5-9.8
[67] GenomicAlignments_1.36.0 systemPipeR_2.6.3        mvtnorm_1.2-3
[70] XML_3.99-0.14            grid_4.3.2               bbmle_1.0.25
[73] amap_0.8-19              bdsmatrix_1.3-6          latticeExtra_0.6-30
[76] edgeR_3.42.4             colorspace_2.1-0         GenomeInfoDbData_1.2.10
[79] restfulr_0.0.15          cli_3.6.1                textshaping_0.3.7
[82] GreyListChIP_1.32.1      fansi_1.0.5              mixsqp_0.3-48
[85] S4Arrays_1.0.6           gtable_0.3.4             DESeq2_1.40.2
[88] digest_0.6.33            ggrepel_0.9.3            farver_2.1.1
[91] rjson_0.2.21             htmlwidgets_1.6.2        htmltools_0.5.6.1
[94] lifecycle_1.0.3          MASS_7.3-60

[Ram]

Please ask https://support.bioconductor.org/