Bioconductor Forum

Hello folks, I tried to use plotVenn() from the DiffBind-package to compare the differential bound sites generated by DESeq, DESeq2 and edgeR. It seems to work - kinda - but...Hello folks, I tried to use plotVenn() from the DiffBind-package to compare the differential bound sites generated by DESeq, DESeq2 and edgeR. It seems to work - kinda - but anyhow

plotvenn

updated 10.4 years ago • N. F.

only recently come across ChIPQC, but I find it incredibly useful, especially in combination with Diffbind. Unfortunately, I can only use some its functionalities at the moment, as I keep encountering an error when I run the

ChIPQC

updated 8.8 years ago • Roger

__(1)__ If I have two chip samples and two input samples, and their fragmentsize are chip\_1,chip\_2,input\_1,input\_1,respectively, should I set the parameter “fragmentSize” as config = data.frame(fragmentSize = c(chip\_1 , chip\_2 , input\_1 , input\_2)) or config = data.frame(fragmentSize = c(chip\_1 , input\_1 , chip\_2 , input\_2) ? The fragmentsize varies among the four sa…

diffbind software error

updated 8.5 years ago • xieyongjun93

Hi, I was reading [this question](https://support.bioconductor.org/p/72385/) and found I have a similar problem to the op, Igor. I'm also trying to figure out the effects of normalization on my data. Initially, I suspect that we would have a global change in our treatment vs control so based on the logic described throughout the literature bFullLibrarySize=TRUE seems appropriate; …

diffbind edger deseq2 chip-seq

updated 9.0 years ago • siklenkak

Hello, Recently I have been asked to run DiffBind with an increased minimum overlap between input regions. I have tested the different between using config$mergeOverlap

DiffBind

updated 21 months ago • Ian D.

Hi, I hope to try a full library size normalization but with edgeR. So I performed the following: ```r data(tamoxifen_analysis) tamoxifen = dba.normalize(tamoxifen, method = DBA_EDGER) dba.normalize(tamoxifen, method = DBA_EDGER, bRetrieve = T) ``` Interestingly the normalization factors are all 1 ``` $norm.method [1] "lib" $norm.factors [1] 1 1 1 1 …

edgeR DiffBind

updated 11 months ago • tifaGis

I am trying to analyze the differential peaks in my ATAC-seq data. I have ATAC-seq analysis on 2 biological conditions with 3 replicates in each condition. Below is my sample info: ``` ID Factor Condition Replicate Intervals 1 ATACctrl1 ctrl1 ctrl 1 8654 2 ATACctrl2 ctrl2 ctrl 2 6750 3 ATACctrl3 ctrl3 ctrl 3 5962 4 ATACe…

DiffBind DESeq2 ATACSeq

updated 21 months ago • lonn

My testing is telling me that for union region generation 1 is the default (a gap), not -1 (1bp overlap). Negative numbers are decreasing as expected, but I am unsure about what the 1bp gap as a default represents. Does a default of mergeOverlap = 1 mean that regions will be merged if they overlap or are up to 1bp away from each other? Thank you, Ian This is the default where config$merge…

DiffBind

updated 17 months ago • Ian D.

Hi, I am trying to look at differential binding of a number of chromatin regulatory proteins via CutandRun only at a **predefined** set of peaks (Approx. 5000 peaks). When I carry out the analysis for different proteins at the same predefined peaks I get a different number of consensus peaks which is always less than 5000. I assumed the analysis would be carried out with the entire predefined…

DiffBind

updated 3.4 years ago • doherta6

I got the following error while trying to create the initiall dba object: ```r > tamoxifen <- dba.count(tamoxifen) Computing summits... Error: Some read files could not be accessed. See warnings for details. In addition: There were 12 warnings (use warnings() to see them) > warnings() Warning messages: 1: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_20…

DiffBind

updated 2.6 years ago • Theo

Hi! I use the function dba.report to retrieve differentially bound sites (th = 1) I found the fold-changes tend to be very small and do not know how to compute them. For example, at one site the mean for control is 1.6973 while the mean for treatment is 4.231, and the Fold is -0.001057009, p-value is 0.0051515283, FDR = 0.99. How the fold-changes were computed? my code is below. Thank you! …

ChIPSeq DiffBind

updated 2.7 years ago • lin.pei26

Not sure what's going on with this function. I assume it's a bug. dba.analyze() ran fine without errors but dba.plotProfile() threw this: ```r > DBA <- dba.analyze(samplesheet, bBlacklist=FALSE, bGreylist=FALSE) Loading sample sheet... 58 1 H3K4me3 AD 1 macs 77 2 H3K4me3 AD 2 macs 78 3 H3K4me3 AD 3 macs 81 4 H3K4me3 AD 4 macs 92 5 H3K4me3 AD 5 macs 145.1 6 H3K4me3 NE 1 ma…

DiffBind

updated 4.4 years ago • bhanratt

cells <- dba(sampleSheet = samples) cells <- dba.count(cells, summits=FALSE) cells <- dba.normalize(cells) cells <- dba.contrast(cells) cells <- dba.analyze(cells) diffbind_deseq <- dba.analyze(cells, bRetrieveAnalysis=TRUE) diffbind_res = results(diffbind_deseq, contrast=c("Tissue", "cell1", "cell2")) report <- dba.report(cells, t…

DESeq2 Diffbind

updated 4.6 years ago • gdolsten

I have a `dba` object which I do not provide as input `bamControl` bam control files, i.e. my `design.csv` file does not have the `bamControl` column. ```r eprint <- dba(sampleSheet = "design.csv",config=data.frame(doBlacklist=FALSE, doGreylist=FALSE)) ``` I then normalize `eprint` in the following manner: ```r eprint <- dba.normalize(eprint,method = DBA_DESEQ2,normalize = DBA_NORM_RLE,b…

DiffBind

updated 4.6 years ago • Alexandre

Dear all, This is the sample sheet, I am using. "SampleID","Tissue","Factor","Condition","Treatment","Replicate","bamReads","Peaks","PeakCaller" "18-133-001_1","MCF7","HSF1","MCF_NHS_changed_hs_1","untreated",1,"s18_133_001_dedup_marked.bam","/lower_bay/home/bony.dekumar/For_Bony/MCF7/filtered_list/s18_133_001_002_NHS_HS_wrt_HSF1allinc_changedHSF1peaks_filtered_1_sorted.bed","raw" "18-133…

DiffBind

updated 6.0 years ago • bony.dekumar

After closer inspection I noticed that Reads and RPKM values for the same samples in dba.counts$peaks changes depending which score metric I use. I was not quite sure if it something that should be expected, If that is the case, than why? My code is: dba.count_NON_INF.Reads <- dba.count( peak.test.NONINF, peaks= GRanges_NonINF, bRemoveDuplicates = FALSE, score = DBA_SCORE_READS ) …

DiffBind

updated 7.6 years ago • Lauma R

Hello, I've got a set of binding site intervals in a DBA object and use dba.count() to count the reads in those peaks. According to the manual, the default score=DBA\_SCORE\_TMM\_MINUS\_FULL. But it also mentions "Note that all raw read counts are maintained for use by dba.analyze". So, the question is, if I then use dba.peakset(bRetrieve=T, DBA\_DATA\_FRAME) to get a dataframe, will …

Diffbind

updated 8.2 years ago • jchap14

Hi there, I want to use DESeq2 for differential peak detection for ChIP-seq data. I know there are many methods implemented for this purpose https://github.com/crazyhottommy/ChIP-seq-analysis\#differential-peak-detection Diffbind internally uses DESeq2 and EdgR, but I want to take the other way: Say I have untreat and treat group for my ChIP-seq data...this purpose https://g…

deseq2 deseq chipseq

updated 8.6 years ago • tangming2005

3. When I load these same samples into DifffBind I am able to conduct the analyses just fine. Using DiffBind I see that the samples that are throwing an error, are those that have low FrIP (5-10%). Perhaps this is the problem?&nbsp

ChIPQC

updated 9.7 years ago • meeta.mistry

eg. there is high variation between control1 and control2 cell types). I have tried using DiffBind using the cell types as blocking factors but that gave me an error (DBA\_FACTOR=Phenotype and DBA\_TREATMENT=cell

design and contrast matrix statistical modeling edger DiffBind

updated 8.9 years ago • bwassie

Hello I hope you are doing well; I am running into this issue when I am trying to run dba.count(). This is the code I am using: ```r #Create a new DBA object using the subset data myDBA <- dba(sampleSheet = subset_data) myDBA <- dba.count(myDBA, bUseSummarizeOverlaps=FALSE) print(myDBA) ``` It does the following: Computing summits... Re-centering peaks... Reads will be count…

DiffBind

updated 2.4 years ago • Mark

Hello! I got such an error report when I include a bed file with no peak into my DBA sample sheet. Error in mergeScores(merged, def, peakset, TRUE) : Not compatible with requested type: [type=character; target=double] Primarily, I do not want to delete this 0-byte bed file from the sample sheet, because its parallel replicates still has some peaks. But if I have to delete it (replicate …

DiffBind

updated 5.0 years ago • ahua217

Hello, I just upgraded diffbind to 2.6.1 using bioconductor 3.6 in my directory under SSH secure shell. I got 12 warnings. Here is information : https...nbsp; other attached packages:  \[1\] BiocInstaller\_1.28.0       DiffBind\_2.6.1              \[3\] SummarizedExperiment\…

bioclite

updated 8.2 years ago • zhaolin20042008

chimera', 'ChIPpeakAnno', 'chopsticks', 'cisPath', 'CNORode', 'ddgraph', 'DESeq2',   'DiffBind', 'easyRNASeq', 'EBImage', 'edgeR', 'flowClust', 'flowCore', 'flowWorkspace', 'gdsfmt', 'GenomicAlignments', 'GenomicFeatures', 'GenomicRanges...casper’ ‘CGEN’   ‘ChemmineR’ ‘chimera’ ‘chopsticks’ ‘cisPath’ ‘CNORode’ ‘ddgraph’ ‘DESeq2’ ‘DiffBind’ ‘EBImage’ ‘edgeR’ ‘flowClust’ ‘fl…

upgrade r update

updated 10.8 years ago • daniil.sarkisyan

To DiffBind users & developers, We have found a bug in dba.overlap introduced _after_ Bioconductor 3.2, and are posting the...nbsp; \[8\] methods   base      other attached packages:  \[1\] DiffBind\_2.4.2             SummarizedExperiment\_1.6.1  \[3\] DelayedArray\_0.2.4…

DiffBind bugs

updated 8.7 years ago • jeremydt

I have a TF which is cytoplasmic in control samples & nuclear under treatment and am intentionally trying to demonstrate that TMM is an inappropriate method in this situation. However, I was quite surprised to see that using DBA_EDGER, the results from DBA_NORM_LIB and DBA_NORM_TMM are 100% identical. Fortunately, the expected differences are evident when using DESeq2, but this seems like the…

DiffBind

updated 2.6 years ago • Stevie Pederson

Hi I'm rerunning some analysis for ATAC since I've been having trouble validating some results. I have two files I created in March of 2022 using Diffbind I installed through conda, an analyzed DBA object and a report-based DBA object where I set fold=1 and th=0.01 When I...I've been having trouble validating some results. I have two files I created in March of 2022 using Diffbind I installed th…

dba.report DiffBind

updated 2.7 years ago • jandrade

Hi, I've been analyzing ATAC-seq data with DiffBind. I have generated a dba object with the samples' bams and the peak bed files resulting from macs. I would like to take

diffbind dba.count dba.peakset

updated 7.8 years ago • pau.rodriguez.sodupe

Hi all: I am trying to analyze zebrafish ATAC seq data using DiffBind. When I run dba.count I get an error like this. Error: Error processing one or more read files. Check warnings(). In addition

DiffBind

updated 4.0 years ago • Ayyappa

Hi I am getting this error message after running dba.count() ```r myDBA <- dba(sampleSheet = subset_data) myDBA <- dba.count(myDBA) 76 neurons CHD4 Ngn2 Ngn2 1 bed Computing summits... Re-centering peaks... Error in colnames(result)[4:ncol(result)] <- colnames(classes) : replacement has length zero In addition: Warning message: Samples have been merged or lost du…

DiffBind

updated 2.4 years ago • Mark

Ideal Probe Hybridization Employing R - DEXSeq: Inference of differential exon usage in RNA-Seq - DiffBind: Differential Binding Analysis of ChIP-Seq peak data - dks: The double Kolmogorov-Smirnov package for evaluating

Transcription Sequencing miRNA qPCR Proteomics Annotation Normalization Visualization cdf

updated 14.3 years ago • Dan Tenenbaum

of my profile plot for Tumor vs Normal. I couldn't decipher the meaning just by reading the diffbind documentation. Here, it seems like the gain curve is above the loss curve for both the tumor and normal. Could anyone

DiffBind

updated 21 months ago • Henry

cairo') > library("ChIPQC") Loading required package: ggplot2 Loading required package: DiffBind Loading required package: GenomicRanges Loading required package: BiocGenerics Loading required package: parallel

chipqc

updated 9.6 years ago • Danielle Denisko

peaks_BD03_ref_data/q_05/BD11_peaks.narrowPeak macs ``` Here is my code ``` library(DiffBind) library(ChIPseeker) library(org.Mm.eg.db) library(bedr) library(ChIPQC) library(BiocParallel) register(SerialParam

ATAC-Seq ChIPQC

updated 7.0 years ago • Subinoy Biswas

ChIPQC\_1.8.3               DiffBind\_2.0.1             SummarizedExperiment\_1.2.3 Biobase\_2.32.0

ChipQC chipqc

updated 9.4 years ago • thekatybrown

to an older version of ChIPQC, but I am having issues with dependencies for older versions of DiffBind. If that's the best solution, I'll make another post. Session info: ------------- > sessionInfo() R version 3.6.1 (2019-07-05) Platform

ChIPQC software error

updated 6.4 years ago • ryleehackley

I get (included sessionInfo() ) Loading required package: ggplot2 Loading required package: DiffBind Loading required package: GenomicRanges Loading required package: methods Loading required package: BiocGenerics...attached packages:  \[1\] ChIPQC\_1.8.2               DiffBind\_2.0.2     &am…

ChIPQC

updated 9.5 years ago • cattapre

_1.26.0       ChIPQC\_1.12.2              DiffBind\_2.4.6             SummarizedExperiment\_1.6.3 DelayedArray\_0.2.7         &nbsp

chipqc

updated 8.6 years ago • woongjaej

Hi DiffBind gurus, I have 4 samples of 4 different tissues. 2 of them treatment, 2 control, here are the main cols of the csv:  SampleID

DiffBind

updated 8.0 years ago • michal.inbar

attached packages:  \[1\] ChIPQC\_1.12.3              DiffBind\_2.4.8             SummarizedExperiment\_1.6.4 DelayedArray\_0.2.7         &nbsp

chipqc

updated 8.4 years ago • psudyant

When I run on a sample individually it runs, but when I add the samplefile it ends in the error listed below. SessionInfo listed at the very bottom. Thanks so much, Tirza Doniger ++++++++++++++++++++ Code: samples = read.csv("chipQC\_samples.csv") BlackListFile <- "mm10.blacklist.bed" exampleExp = ChIPQC(samples,annotation="mm10",blacklist = BlackListFile,consensus=TRUE,bcount=FA…

software error chipqc

updated 8.6 years ago • tirza.doniger

Hello, I have the following samples, with three replicates in each of them:

Time point	Population	Genotype1	Genotype2
00h	Precursor	WT	KO
06h	Subset A	WT	KO
18h	Subset A	WT	KO
72h	Subset A	WT	KO
06h	Subset B	WT	KO
18h	Subset B	WT	KO
72h	Subset B	WT	KO

My biological setup: * I started with 2 samples of Precursor (considered also as 00h): KO or WT. * …

diffbind R atac-seq

updated 7.3 years ago • Firas

If choosing EDGER for my dab object should I choose one of the TMM normalized score categories in dba.count? Trying to figure out which of the these categories makes most sense for my ATAC-seq data. Thanks!

diffbind

updated 9.0 years ago • rbronste

Hi [Rory][1], I am unable to control the text size for colAttributes in the annotation bar for dbaplot() or dba.plotHeatmap(). Can you or anyone please guide how should I do the same. Ill really appreciate your help. Thanks [1]: https://support.bioconductor.org/u/5741/

diffbind dbaplot() dba.plotHeatmap()

updated 6.2 years ago • researcher

Hi, I have a list of differentially bound sites between conditions and would like to export lists defined by 2 things: fold change between some positive or negative value given the condition and specific FDR cutoffs. If anyone has advice on how to go about this would be huge help, thanks so much! Rob

diffbind

updated 9.0 years ago • rbronste

I have ChIP-seq datasets as the following:

	Cell	Type	Condtion
1	A	Input	WT
2	A	Pulldown	WT
3	B	Input	WT
4	B	Pulldown	WT
5	C	Input	MT
6	C	Pulldown	MT
7	D	Input	MT
8	D	Pulldown	MT

I would like to find differential region of pulldown between WT and MT in condition after controlling individual cells and types. I thought the design formula: ~ Cell + Type + …

deseq2 diffbind

updated 7.5 years ago • bioinfo

Hi I am analyzing ATAC-seq data for 12 samples. My sample sheet looks as follows (for the first sample): __Sample ID Tissue Replicate BamReads Peaks PeakCaller__ Sample1 FL 1.1 /home/stark/Documents/Rachelle/sample1\_trimmed\_rmdup\_bowtie2\_mapped.b…

diffbind dba.count

updated 8.3 years ago • VCLRAC001

I'm getting the following error and I'm not sure why. Any help would be appreciated. > my.DB2 = dba.report(mydata, bCounts=TRUE) Error in .Call2("solve\_user\_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 1: range cannot be determined from the supplied arguments (too many NAs) I also got a warning message at the dna.analyze step: > mydata = dba.analyze(m…

diffbind

updated 10.7 years ago • mm2489

Hi I am analyzing ATAC-seq data for several embryonic replicates. An extract of my sample sheet looks as follows: __Sample ID Tissue Replicate BamReads Peaks PeakCaller__ Sample1 FL 1.1 /home/stark/Documents/Rachelle/sample1\_trimmed\_rmdup\_bowtie2\…

diffbind dba.count atac-seq

updated 8.3 years ago • VCLRAC001

Hi Rory, I am trying to analyze my chipseq data of H3K4me3 with 4 conditions and 2 replicates. I have only 1 replicate for input. I think I create the sample sheet correctly and it works until some points but in dba.analyze part I get error as following. H3K4me3\_narrow <- read.csv("chipseq\_rep1\_rep2.csv") H3K4me3\_narrow <- dba(sampleSheet = "chipseq\_rep1\_rep2.csv") pl…

diffbind

updated 10.2 years ago • khani.sajjad

I am using the following command: ``` > plot(DBdata,cexRow=2,cexCol=2,dendrogram='none',lhei = c(0.5,6),lwid = c(0.5,4), ColAttributes=c(DBA_TREATMENT,DBA_CONDITION),key=F, colSideCols=list(c("lightpink","skyblue"),c("chocolate","darkgrey","darkorchid4"))) ``` but unable to control the font size for the ColAttributes in the annotation bar. Any help or suggestion will be highly appr…

diffbind colattributes chipseq cex

updated 6.2 years ago • researcher

Hi, I cannot find the way to get the coordination for the summits of my peaks. I added the summit option to the dba.count and I am looking at the dba.peakset documentation and cannot figure out how to get the data.. Is there a way to get the summits of the peaks together with the differential affinity data when using dba.report? Thanks

diffbind

updated 7.4 years ago • Udi Landau

Hello, am trying to import bed files from MACS2 peak calling with dba.peakset function. I have 3 files and i would like to import in this way: mESC <- dba.peakset(NULL,peaks="/home/tandrean/Desktop/Gadd45-TKO/4.test\_peaks.narrowPeak", peak.caller="bed", peak.format= "narrow",sampID="Gadd45.TKO.1",tissue="mESC",…

diffbind dba.peakset

updated 9.0 years ago • fusion.slope

Hi After pulling up a list of differentially bound peaks with __View__ in R, wondering how you sort by the index rather than one of the categories such as fold change? Thanks. Rob

R diffbind

updated 8.8 years ago • rbronste

Hi, When I try to calculate the overlap rate between peaksets, I get the following errors: > names(broad_gtsf1$masks) # just list all [1] "K562" "H3K9Me3" "75" "313" "WT" "Mutant" "counts" "Consensus" "Replicate.1" "Replicate.2" "Replicate.3" "Replicate.4" "All" [14] "None" > dba.overlap(broad_gtsf1, …

diffbind

updated 6.7 years ago • aviv.de-morgan

How can I control colors for different colAttributes: one as Factor and other is Condition. Can I use different colors for these two cola attributes? Additionally, How can I have the color annotation for each factor and condition. Kindly help. Thanks!

diffbind plot plotHeatmap

updated 6.5 years ago • researcher

Hi! When I use the function dba to create a dba object, I always encounter the error :

Error in if (file.info(peaks)$size > 0) { : 
  missing value where TRUE/FALSE needed

my code is :

a <- dba(sampleSheet = 'samplesheet.csv')

and the samplesheet.csv is as follows :

SampleID

Tissue

Factor

Condition

Treatment

Replicate

bamReads

ControlID

bamControl

Peak…

diffbind

updated 8.0 years ago • xieyongjun93

I am trying to get some clarity on dba.count and dba.analyze. 1) For dba.count, does the function look at overlapping peaks and instead of using the score assigned by the peak caller (which I understand dba() does), it uses the number of reads found at that peak for a sample and calculates how well the reads correlate with that of the same peak in another sample? Or does it just look overa…

diffbind

updated 10.5 years ago • JKUMAR12

Hello, I would like to clarify what are the units of the "Conc" columns and also the read counts column if we set `` bCounts=T ``. For my analysis, I performed `` dba.count() `` with `` score=DBA_SCORE_RPKM `` and `` dba.analyze() `` with method=DBA\_DESEQ2. When I call dba.report(DBA, contrast = 1, th=0.05, fold = 1.5, bCalled = T, bCalledDetail = T, bCounts = T) 1. Are the concentra…

diffbind

updated 7.3 years ago • Shamaine

Bioconductors: We are pleased to announce Bioconductor 2.14, consisting of 824 software packages, 200 experiment data packages, and more than 860 up-to-date annotation packages. There are 77 new software packages, and many updates and improvements to existing packages; Bioconductor 2.14 is compatible with R 3.1.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release in…

BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage

updated 11.8 years ago • Dan Tenenbaum