Not able to replicated Diffbind example dataset.
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Entering edit mode
Ayyappa ▴ 10
@768f3a7c
Last seen 10 weeks ago
United States

Happy new year folks !!!

I used the Diffbind vignette and ran the commands provided in Rstudio.

However, the Intervals in the dba object do not match with the ones provided in the vignette. It would be great if you could help me out with this. Thanks in advance.

dba object in Diffbind vignette

> tamoxifen
11 Samples, 2845 sites in matrix (3795 total):
ID Tissue Factor Condition Treatment Replicate Intervals
1 BT4741 BT474 ER Resistant Full-Media 1 1080
2 BT4742 BT474 ER Resistant Full-Media 2 1122
3 MCF71 MCF7 ER Responsive Full-Media 1 1556
4 MCF72 MCF7 ER Responsive Full-Media 2 1046
5 MCF73 MCF7 ER Responsive Full-Media 3 1339
6 T47D1 T47D ER Responsive Full-Media 1 527
7 T47D2 T47D ER Responsive Full-Media 2 373
8 MCF7r1 MCF7 ER Resistant Full-Media 1 1438
9 MCF7r2 MCF7 ER Resistant Full-Media 2 930
10 ZR751 ZR75 ER Responsive Full-Media 1 2346
11 ZR752 ZR75 ER Responsive Full-Media 2 2345

dba object when I run it in my system

> tamoxifen
11 Samples, 2845 sites in matrix (3795 total):
       ID Tissue Factor  Condition  Treatment Replicate Intervals
1  BT4741  BT474     ER  Resistant Full-Media         1         2
2  BT4742  BT474     ER  Resistant Full-Media         2         3
3   MCF71   MCF7     ER Responsive Full-Media         1         6
4   MCF72   MCF7     ER Responsive Full-Media         2         1
5   MCF73   MCF7     ER Responsive Full-Media         3         4
6   T47D1   T47D     ER Responsive Full-Media         1        10
7   T47D2   T47D     ER Responsive Full-Media         2         9
8  MCF7r1   MCF7     ER  Resistant Full-Media         1         5
9  MCF7r2   MCF7     ER  Resistant Full-Media         2        11
10  ZR751   ZR75     ER Responsive Full-Media         1         8
11  ZR752   ZR75     ER Responsive Full-Media         2         7

This is what the Rstudio console displays

library(DiffBind) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter,
Find, get, grep, grepl, intersect, is.unsorted, lapply, Map,
mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit,
which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:grDevices’:

windows

Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins,
colOrderStats, colProds, colQuantiles, colRanges, colRanks,
colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs,
colVars, colWeightedMads, colWeightedMeans,
colWeightedMedians, colWeightedSds, colWeightedVars,
rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse,
rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums,
rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs,
rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs,
rowVars, rowWeightedMads, rowWeightedMeans,
rowWeightedMedians, rowWeightedSds, rowWeightedVars

Loading required package: Biobase Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages
'citation("pkgname")'.

Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

rowMedians

The following objects are masked from ‘package:matrixStats’:

anyMissing, rowMedians

DiffBind 3.0 includes substantial updates. See ?DiffBind3 for details on what has changed. Warning messages: 1: In options(stringsAsFactors = TRUE) : 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled 2: package ‘DiffBind’ was built under R version 4.0.4 3: package ‘BiocGenerics’ was built under R version 4.0.5 4: package ‘GenomeInfoDb’ was built under R version 4.0.5 5: package ‘matrixStats’ was built under R version 4.0.5

setwd(system.file('extra',package='DiffBind'))

samples <- read.csv(file.path(system.file("extra", package="DiffBind"), "tamoxifen.csv"))

tamoxifen <- dba(sampleSheet=samples) BT4741 BT474 ER Resistant Full-Media 1 bed BT4742 BT474 ER Resistant Full-Media 2 bed MCF71 MCF7 ER Responsive Full-Media 1 bed MCF72 MCF7 ER Responsive Full-Media 2 bed MCF73 MCF7 ER Responsive Full-Media 3 bed T47D1 T47D ER Responsive Full-Media 1 bed T47D2 T47D ER Responsive Full-Media 2 bed MCF7r1 MCF7 ER Resistant Full-Media 1 bed MCF7r2 MCF7 ER Resistant Full-Media 2 bed ZR751 ZR75 ER Responsive Full-Media 1 bed ZR752 ZR75 ER Responsive Full-Media 2 bed

tamoxifen 11 Samples, 2845 sites in matrix (3795 total): ID Tissue Factor Condition Treatment Replicate Intervals 1 BT4741 BT474 ER Resistant Full-Media 1 2 2 BT4742 BT474 ER Resistant Full-Media 2 3 3 MCF71 MCF7 ER Responsive Full-Media 1 6 4 MCF72 MCF7 ER Responsive Full-Media 2 1 5 MCF73 MCF7 ER Responsive Full-Media 3 4 6 T47D1 T47D ER Responsive Full-Media 1 10 7 T47D2 T47D ER Responsive Full-Media 2 9 8 MCF7r1 MCF7 ER Resistant Full-Media 1 5 9 MCF7r2 MCF7 ER Resistant Full-Media 2 11 10 ZR751 ZR75 ER Responsive Full-Media 1 8 11 ZR752 ZR75 ER Responsive Full-Media 2 7

DiffBind • 254 views
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2
Entering edit mode
Rory Stark ★ 4.4k
@rory-stark-5741
Last seen 6 days ago
CRUK, Cambridge, UK

I'm not 100% sure what is going on, but based on the load message ("DiffBind 3.0 includes substantial updates..."), you are using an older version. What is the output of sessionInfo()?

The currently released version is 3.4, perhaps you can update your Bioconductor and DiffBind versions and try again?

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0
Entering edit mode

Thank you for the reply Rory. I updated Diffbind to ver 3.4 and ran the vignette example again, but got the same result.

Here is the session info

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252
[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C
[5] LC_TIME=English_India.1252

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

other attached packages: [1] DiffBind_3.4.4 SummarizedExperiment_1.20.0 [3] Biobase_2.50.0 MatrixGenerics_1.2.1
[5] matrixStats_0.61.0 GenomicRanges_1.42.0
[7] GenomeInfoDb_1.26.7 IRanges_2.24.1
[9] S4Vectors_0.28.1 BiocGenerics_0.36.1

loaded via a namespace (and not attached): [1] rappdirs_0.3.3
[2] JASPAR2018_1.1.1
[3] rtracklayer_1.49.5
[4] AnnotationForge_1.32.0
[5] R.methodsS3_1.8.1
[6] coda_0.19-4
[7] tidyr_1.1.4
[8] ggplot2_3.3.5
[9] bit64_4.0.5
[10] knitr_1.37
[11] irlba_2.3.5
[12] DelayedArray_0.16.3
[13] R.utils_2.11.0
[14] data.table_1.14.2
[15] hwriter_1.3.2
[16] KEGGREST_1.30.1
[17] TFBSTools_1.28.0
[18] RCurl_1.98-1.5
[19] generics_0.1.1
[20] GenomicFeatures_1.42.3
[21] cowplot_1.1.1
[22] lambda.r_1.2.4
[23] RSQLite_2.2.9
[24] shadowtext_0.1.1
[25] bit_4.0.4
[26] tzdb_0.2.0
[27] enrichplot_1.10.2
[28] base64url_1.4
[29] xml2_1.3.3
[30] assertthat_0.2.1
[31] batchtools_0.9.15
[32] DirichletMultinomial_1.32.0
[33] viridis_0.6.2
[34] amap_0.8-18
[35] apeglm_1.12.0
[36] xfun_0.29
[37] hms_1.1.1
[38] rJava_1.0-6
[39] evaluate_0.14
[40] fansi_0.5.0
[41] progress_1.2.2
[42] caTools_1.18.2
[43] dbplyr_2.1.1
[44] Rgraphviz_2.34.0
[45] igraph_1.2.10
[46] DBI_1.1.2
[47] htmlwidgets_1.5.4
[48] futile.logger_1.4.3
[49] purrr_0.3.4
[50] ellipsis_0.3.2
[51] corrplot_0.92
[52] dplyr_1.0.7
[53] backports_1.4.1
[54] Rbowtie2_1.12.0
[55] V8_4.0.0
[56] annotate_1.68.0
[57] biomaRt_2.46.3
[58] vctrs_0.3.8
[59] cachem_1.0.6
[60] withr_2.4.3
[61] ggforce_0.3.3
[62] DOT_0.1
[63] BSgenome_1.58.0
[64] bdsmatrix_1.3-4
[65] checkmate_2.0.0
[66] GenomicAlignments_1.26.0
[67] prettyunits_1.1.1
[68] pipeFrame_1.6.0
[69] DOSE_3.16.0
[70] seqLogo_1.56.0
[71] crayon_1.4.2
[72] genefilter_1.72.1
[73] edgeR_3.32.1
[74] pkgconfig_2.0.3
[75] tweenr_1.0.2
[76] rlang_0.4.10
[77] lifecycle_1.0.1
[78] downloader_0.4
[79] BiocFileCache_1.14.0
[80] GOstats_2.56.0
[81] VennDiagram_1.7.1
[82] invgamma_1.1
[83] rsvg_2.1.2
[84] polyclip_1.10-0
[85] graph_1.68.0
[86] Matrix_1.4-0
[87] ashr_2.2-47
[88] boot_1.3-28
[89] pheatmap_1.0.12
[90] png_0.1-7
[91] viridisLite_0.4.0
[92] rjson_0.2.21
[93] bitops_1.0-7
[94] R.oo_1.24.0
[95] KernSmooth_2.23-17
[96] visNetwork_2.1.0
[97] Biostrings_2.58.0
[98] blob_1.2.2
[99] mixsqp_0.3-43
[100] stringr_1.4.0
[101] SQUAREM_2021.1
[102] qvalue_2.22.0
[103] ShortRead_1.48.0
[104] brew_1.0-6
[105] readr_2.1.1
[106] jpeg_0.1-9
[107] CNEr_1.26.0
[108] scales_1.1.1
[109] memoise_2.0.1
[110] GSEABase_1.52.1
[111] magrittr_2.0.1
[112] plyr_1.8.6
[113] gplots_3.1.1
[114] zlibbioc_1.36.0
[115] compiler_4.0.3
[116] scatterpie_0.1.7
[117] tinytex_0.36
[118] bbmle_1.0.24
[119] RColorBrewer_1.1-2
[120] plotrix_3.8-2
[121] Rsamtools_2.6.0
[122] systemPipeR_1.24.6
[123] XVector_0.30.0
[124] Category_2.56.0
[125] formatR_1.11
[126] MASS_7.3-53
[127] tidyselect_1.1.1
[128] stringi_1.7.6
[129] emdbook_1.3.12
[130] yaml_2.2.1
[131] GOSemSim_2.16.1
[132] askpass_1.1
[133] locfit_1.5-9.4
[134] latticeExtra_0.6-29
[135] ggrepel_0.9.1
[136] grid_4.0.3
[137] VariantAnnotation_1.36.0
[138] fastmatch_1.1-3
[139] tools_4.0.3
[140] rstudioapi_0.13
[141] TFMPvalue_0.0.8
[142] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [143] gridExtra_2.3
[144] farver_2.1.0
[145] ggraph_2.0.5
[146] digest_0.6.29
[147] rvcheck_0.2.1
[148] BiocManager_1.30.16
[149] pracma_2.3.6
[150] motifmatchr_1.12.0
[151] Rcpp_1.0.7
[152] httr_1.4.2
[153] AnnotationDbi_1.52.0
[154] colorspace_2.0-0
[155] XML_3.99-0.8
[156] truncnorm_1.0-8
[157] splines_4.0.3
[158] yulab.utils_0.0.4
[159] RBGL_1.66.0
[160] graphlayouts_0.7.2
[161] xtable_1.8-4
[162] jsonlite_1.7.2
[163] futile.options_1.0.1
[164] poweRlaw_0.70.6
[165] tidygraph_1.2.0
[166] ggfun_0.0.4
[167] R6_2.5.1
[168] pillar_1.6.4
[169] htmltools_0.5.2
[170] glue_1.4.2
[171] fastmap_1.1.0
[172] clusterProfiler_3.18.1
[173] BiocParallel_1.24.1
[174] ChIPseeker_1.26.2
[175] fgsea_1.16.0
[176] GreyListChIP_1.22.0
[177] mvtnorm_1.1-3
[178] utf8_1.2.2
[179] lattice_0.20-41
[180] tibble_3.1.6
[181] esATAC_1.12.0
[182] numDeriv_2016.8-1.1
[183] curl_4.3.2
[184] gtools_3.9.2
[185] GO.db_3.12.1
[186] openssl_1.4.6
[187] survival_3.2-13
[188] limma_3.46.0
[189] rmarkdown_2.11
[190] munsell_0.5.0
[191] DO.db_2.9
[192] GenomeInfoDbData_1.2.4
[193] reshape2_1.4.4
[194] gtable_0.3.0

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0
Entering edit mode

Hi Rory:

I had updated the R version and Rstudio version. Now the vignette seems to be working fine.

Thank you.

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