Difference in Contrast in DiffBind
0
0
Entering edit mode
zzrammal • 0
@9ae4560e
Last seen 11 days ago
France

Hello everyone, I have a simple question; I am doing a DiffBind analysis and using dba.contrast function what's the difference if we do in diffBind contrast ie: WT vs Control and Control vs WT? normally there should not be any differences but when i did it, i saw a differences in Fold and even in the number of sites. Thank u!

sessionInfo( )

sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS

Matrix products: default BLAS/LAPACK: /shared/ifbstor1/software/miniconda/envs/r-4.1.1/lib/libopenblasp-r0.3.18.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] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] rtracklayer_1.54.0 TxDb.Hsapiens.UCSC.hg38.knownGene_3.14.0 [3] GenomicFeatures_1.46.1 AnnotationDbi_1.56.1
[5] DiffBind_3.4.11 BiocParallel_1.28.3
[7] BiocManager_1.30.23 openxlsx_4.2.5.2
[9] readxl_1.4.3 EnhancedVolcano_1.13.2
[11] ggrepel_0.9.1 magrittr_2.0.3
[13] lubridate_1.9.3 forcats_1.0.0
[15] stringr_1.5.1 dplyr_1.1.4
[17] purrr_1.0.2 readr_2.1.5
[19] tidyr_1.3.1 tibble_3.2.1
[21] tidyverse_2.0.0 DESeq2_1.34.0
[23] SummarizedExperiment_1.24.0 MatrixGenerics_1.6.0
[25] matrixStats_0.62.0 GenomicRanges_1.46.1
[27] GenomeInfoDb_1.30.1 IRanges_2.28.0
[29] S4Vectors_0.32.4 Biobase_2.54.0
[31] BiocGenerics_0.40.0 limma_3.50.3
[33] ggplot2_3.5.1

loaded via a namespace (and not attached): [1] amap_0.8-19 colorspace_2.0-3 rjson_0.2.20 hwriter_1.3.2
[5] XVector_0.34.0 rstudioapi_0.16.0 bit64_4.0.5 fansi_1.0.3
[9] mvtnorm_1.1-3 apeglm_1.16.0 xml2_1.3.3 splines_4.1.1
[13] cachem_1.0.6 geneplotter_1.72.0 Rsamtools_2.10.0 annotate_1.72.0
[17] dbplyr_2.1.1 ashr_2.2-47 png_0.1-7 GreyListChIP_1.26.0
[21] compiler_4.1.1 httr_1.4.4 assertthat_0.2.1 Matrix_1.3-4
[25] fastmap_1.1.0 cli_3.6.2 prettyunits_1.1.1 htmltools_0.5.2
[29] tools_4.1.1 coda_0.19-4 gtable_0.3.1 glue_1.6.2
[33] GenomeInfoDbData_1.2.7 systemPipeR_2.0.4 rappdirs_0.3.3 ShortRead_1.52.0
[37] Rcpp_1.0.9 bbmle_1.0.24 cellranger_1.1.0 vctrs_0.6.5
[41] Biostrings_2.62.0 irlba_2.3.5.1 timechange_0.3.0 lifecycle_1.0.3
[45] restfulr_0.0.13 gtools_3.9.3 XML_3.99-0.9 edgeR_3.36.0
[49] zlibbioc_1.40.0 MASS_7.3-54 scales_1.3.0 BSgenome_1.62.0
[53] hms_1.1.3 parallel_4.1.1 RColorBrewer_1.1-3 curl_4.3.3
[57] yaml_2.3.6 memoise_2.0.1 emdbook_1.3.12 biomaRt_2.50.0
[61] bdsmatrix_1.3-7 latticeExtra_0.6-29 stringi_1.7.8 RSQLite_2.2.8
[65] SQUAREM_2021.1 genefilter_1.76.0 BiocIO_1.4.0 filelock_1.0.2
[69] caTools_1.18.2 zip_2.2.0 truncnorm_1.0-8 rlang_1.1.3
[73] pkgconfig_2.0.3 bitops_1.0-7 lattice_0.20-45 invgamma_1.1
[77] GenomicAlignments_1.30.0 htmlwidgets_1.5.4 bit_4.0.4 tidyselect_1.2.1
[81] plyr_1.8.7 R6_2.5.1 gplots_3.1.3.1 generics_0.1.3
[85] DelayedArray_0.20.0 DBI_1.1.2 pillar_1.9.0 withr_2.5.0
[89] mixsqp_0.3-43 survival_3.2-13 KEGGREST_1.34.0 RCurl_1.98-1.9
[93] crayon_1.5.2 KernSmooth_2.23-20 utf8_1.2.2 BiocFileCache_2.2.0
[97] tzdb_0.2.0 progress_1.2.2 jpeg_0.1-9 locfit_1.5-9.4
[101] grid_4.1.1 blob_1.2.2 digest_0.6.30 xtable_1.8-4
[105] numDeriv_2016.8-1.1 munsell_0.5.0
```

DiffBind • 66 views
ADD COMMENT

Login before adding your answer.

Traffic: 818 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