Not able to replicated Diffbind example dataset.
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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

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