Bioconductor Forum

Hello,  I am very new with DiffBind, so pardon me if it is a silly question. I am trying to compare our ChIP-seq data with a published data set (GEO GSE322222...and they only provided BED files. I am wondering if it is possible to use DiffBind when we don't have access to BAM files (read and control). Thanks, Hosna

diffbind

updated 6.7 years ago • jabbari

about the interpretation of the colours assigned to the dots in the MA plots obtained with the DiffBind package: red dots represent significantly differentially bound sites but what about the dark blue dots, the ones

diffbind maplot

updated 6.3 years ago • grundelphine

When you run `` dba.contrast `` and `` dba.analyze `` in DiffBind, it divides the samples into all the possible groups and compares the various groups. If you have paired samples...When you run `` dba.contrast `` and `` dba.analyze `` in DiffBind, it divides the samples into all the possible groups and compares the various groups. If you have paired samples (for

diffbind

updated 9.3 years ago • igor

chr1 4785666 4785667 BMDM-RNAPIIpS2-CTR-1-ChIPseq-GTACACCT_S9_L003_R1_001_peak_1 18.38304 And my DiffBind call us ctr <- dba.peakset(NULL, peaks="BMDM-RNAPIIpS2-CTR-1-ChIPseq-GTACACCT_S9_L003_R1_001_summits.bed", peak.caller...peaks)$size > 0) { : missing value where TRUE/FALSE needed" What is the issue? I'm new to DiffBind …

DiffBind Peakset

updated 4.1 years ago • hkitano

to the other. However, whenever I compare counts from the consensus peakset generated by DiffBind, the dramatic difference is gone. I don't exactly understand the source of discrepancy between IGV peak intensities...and DiffBind counts. I would really appreciate your help &nbsp

diffbind

updated 9.0 years ago • mm2489

Dear all,        We are using Diffbind to examine differential peak enrichment between male and female samples. Our input control is from the same sample...before the immunoprecipitation stage. We have 4 replicates per treatment. The way we are using the Diffbind commands is exactly like given in the vignette and the manual. It is our unders…

diffbind

updated 8.3 years ago • surjray

Hi, so I have obtained using the package diffBind a set of regions with significant differential signal between 2 conditions. In the diffbind report, there is a column

diffBind Fold Change

updated 3.0 years ago • joseluis.ruiz

like a general question. Can anyone specify how to properly give multiple covariate information in DiffBind and analyse accordingly? I have human samples with multiple metadata, i.e. age, sex, post mortem delay, sample pH, disease...of interest at the last of the model to correct for all the covariates." my questions: 1. Will DiffBind work like that? I remember from the Vignette, about using …

DiffBind Deseq2

updated 3.5 years ago • bioinfouser2

example code from the [link ][1] I am getting error as mentioned below, I succesfully installed the diffbind I am thinking its issue with reading file with the dba.analyze ```library(DiffBind) setwd(system.file('extra',package...DiffBind')) tamoxifen <- dba.analyze("tamoxifen.csv")``` sessionInfo( ) error Error: $ operator is invalid for atomic vectors help...the is…

DiffBind

updated 3.2 years ago • Lucky

When running dba.normalize in diffbind I am receiving the follow error: ```if (!requireNamespace("BiocManager", quietly = TRUE))``` ```install.packages("BiocManager...BiocManager::install("DiffBind")``` ```library(DiffBind)``` # Load sample sheet ```sampleSheet <- read.csv("/Users/vwimalasena/Documents/Ewald/ChIP-seq/DiffBind...Create a DBA object ```dbaObj <- dba(sampleSheet="/…

DiffBind Errorinsocketconnection SpikeIn

updated 12 days ago • Virangika

Goodmorning, I would like to perform Differential Binding Analysis in the following situation: - I have a dataset derived from experimental data I have processed on my own and for which I have already done the differential analysis using DiffBind - I know would like to integrate a second dataset derived from literature, for that I would like to use pre-calculated peak counts: I have a peak…

ATACSeq DiFFBind

updated 3.0 years ago • Riba Michela

Hi,  Can I use HOMER called peaks in DiffBind without making any changes to the peaks file (HOMER output file)?   Thank you &nbsp

diffbind HOMER

updated 6.4 years ago • Hesh

The default behavior of DiffBind when merging peaks from different samples is that peaks with at least 1 bp overlap will be merged. For example, peak...overlap between the two peaks, so the above example won't merge? If anyone knows how to do this in DiffBind or ways using other R packages that would still be compatible with other parts of DiffBind, that would be great. Thank

DiffBind ChIPseq

updated 3.0 years ago • zhenfeng.liu1

Hello, I installed "DiffBind" today and am going through the example exercise, although I cannot get very far.  I am getting an error message...dba"" I downloaded the newest version of R (3.3.2) on OSX and reinstalled Bioconductor base and DiffBind and still no luck. Thanks very much, Rebecca &nbsp

DiffBind dba package installation

updated 7.5 years ago • rebecca.spokony

span style="line-height:1.6">Hello, I am using DiffBind to find differential binding sites for different ChIP-seq proteins. The experimental workflow consists to treat...how it will be the best way to analyse the data in DiffBind. I saw that I can introduce a column in the csv t…

DiffBind diffbind

updated 9.5 years ago • sergio.espeso-gil

Hello, Dr Stark. Recently, I am learning some knowlege about coordinate system of zero based and one based. And It reminds me that I often do some format change in DiffBind :). Just like **1. change the merged coordinate into bed format** ```r dba_meta <- dba(minOverlap = 1, sampleSheet = sample_info) ``` ```r > dba_meta$merged[1:10,] CHR START END 1 1 30…

diffbind Rory Stark coordinate

updated 4.1 years ago • shangguandong1996

samples) dbObj <- dba.count(dbObj, bUseSummarizeOverlaps=TRUE) ``` I use the hg38 genome for diffbind is OK, while wheat genome is so big, how can use diffbind to analyze the wheat project

DiffBind

updated 7 months ago • zgyu12

I am using DiffBind and trying to export the matrix of values for all peaks. If I use `` dba.report() `` with `` bcounts=TRUE ``, I get those values, but

diffbind

updated 7.6 years ago • igor

Wondering if the basic matrix output from dba.count in DiffBind would be an appropriate input matrix into DESeq2 (via DESeqDataSetFromMatrix) or if has to be modified in some...other fashion? I want to run DESeq2 interactions on this interval read count matrix generated by DiffBind. Thank you

deseq2 diffbind

updated 6.5 years ago • rbronste

In the `DiffBind` package, how can I extract the t-statistic from the `dba.report

r DiffBind ATAC

updated 4.2 years ago • lindsaynhayes

I am using DiffBind for differential occupancy analysis for my Chip-seq data set. The problem I am having is that- as of last week, whenever...4 overlapping rates (82695,51554,34786,24150). However, When I tried running the code today (updated DiffBind to version 2.8.0), I am getting the following numbers. The first two numbers are the same from dba.overlap function...ran the Tamoxifen vignette a…

DiffBind dba.overlap

updated 5.7 years ago • romicakerketta

are now studying chromatin modification signature in normal vs disease human samples and found that DiffBind worked really well for our purpose. Manual tells me that DiffBind uses the same statistics of EdgeR to find differential...bound site, but I'm not sure how DiffBind treats those factors specific for ChIP-seq analysis. 1) Input reads There seems to be some function like bScaleCont…

diffbind

updated 8.7 years ago • yfyuzawa

Hi everyone, wanted to run my open chromatin mapping methodology with DiffBind by you and see if there is room for improvement. Basically have 3-4 replicates per experiment where the vast majority...runs. __Running the following:__ samples <- read.csv(file.path(system.file("extra", package="DiffBind"),"RPMG\_DNAse.csv")) RPMG<- dba(minOverlap = 2, sampleSheet = "RPMG\_DNAse.csv",…

diffbind dnaseseq atac-seq

updated 7.3 years ago • rbronste

May I know how DiffBind analyze peak present/absent data for a PCA analysis? The traditional PCA needs continuous values with the...May I know how DiffBind analyze peak present/absent data for a PCA analysis? The traditional PCA needs continuous values with the&nbsp...normal distribution. Does DiffBind use a non-parametric method? Or DiffBind use scores (e.g. FDR value) for …

DiffBind

updated 3.5 years ago • Gary

and bioconductor support, there doesn't seem to be a way to specify a custom normalization factor in DiffBind when analyzing using DESeq2. I'm wondering if there is a relatively easy "hacky" way to do this? Thanks in advance for

diffbind

updated 3.5 years ago • C T

Hello! Is it possible to plot principal components 3 and 4 with Diffbind plotPCA function? - thanks

PCA DiffBind

updated 3.2 years ago • alessandrotestori7

Hi, I had a question about which values to use for the scoreCol when generating a dba object in DiffBind. My peak files are SICER islandSummary files, which contain columns for pvalue, fold change, and FDR. Currently, I have...the fold change values from my peak files (column 8). Is it best to use fold changes as input into DiffBind, or would pvalues or FDR be a better score to use? Thanks…

DiffBind ChIPSeq chipseq

updated 2.4 years ago • erbrocato

How can I correct continuous variable (eg: age) in diffbind? I find that in my data age is a covariate that I need to correct for. The column TISSUE is used for AGE in my data. I tried...the contrast and then running dba.analyze but I get 0 peaks after blocking AGE. ``` library(DiffBind) library(DESeq2) library(edgeR) library(GenomicAlignments) > chip1 21 Samples, 200401 site…

diffbind deseq2

updated 5.2 years ago • janani.sundaresan

Hi, I have been trying to use the DiffBind for analyzing my ChIP-seq data; during the dba.contrast step, I came across an error that I show below. > H3K4me3 &lt

diffbind

updated 5.9 years ago • bright602

Dear Rory, I read peaksets to DiffBind as follows: wt <- dba.peakset(NULL, peaks = system.file("/home/labs/shlush/avivdm/chipseq_313_75/9_macs_broad/wt1_ip_chip_7...5.NOMOD_peaks.broadPeak", package = "DiffBind"), peak.caller = "narrow", sampID="WT1_75", tissue = "K562", factor = "H3K9Me3", condition = "75", replicate = 1) wt <- dba.peakset(wt, peaks…

DiffBind consensus

updated 4.9 years ago • aviv.de-morgan

Hello: Dose anyone have experiences in using DiffBind for spike-in normalization? I have dm6 spike-in for both input and IP samples. I have aligned bam files for each sample...Hello: Dose anyone have experiences in using DiffBind for spike-in normalization? I have dm6 spike-in for both input and IP samples. I have aligned bam files for each sample with both human and drosophila genomes, i.e, …

DiffBind

updated 18 months ago • yuhuihui2011

I used macs2 callpeak for peak calling and then used the .bam files and .narrowPeak files to apply Diffbind and get the binding matrix. Also, I'm working with DiffBind_2.14.0. I need to mention that the bam files have gone through...overlapping ones, and then annotated all the regions but HOXa was not found. So, I believe that DiffBind is filtering some of the regions somehow. My question is tha…

ATACSeq DiffBind

updated 2.9 years ago • sh.kazempour94

Hi, I don't have experience with R, so I ran Diffbind using Galaxy. I didn't specify the Summit option, so all my peaks have a different width. Now I want to get the summits...of the differential peaks to run motif analysis. Is there an easy way to do this from the Diffbind output files? Thank you

DiffBind

updated 3.0 years ago • fbleao

enlarge the plot pane. I also see that you are using a somewhat dated version of R and hence of the DiffBind (and all other Bioconductor) packages. If possible, you may want to try updating to the most recent released version...June 04, 2014 1:13 AM >To: ??? >Cc: Rory Stark >Subject: Re: Could yo help us about DiffBind error > >Hi, Gary, > >Try te…

DiffBind DiffBind

updated 9.9 years ago • Rory Stark

cbind, scores) ``` Best wishes Guandong Shang And I have another confuse about the DiffBind [Question: The coordinate system problem about DiffBind output](https://support.bioconductor.org/p/128515/) if you

diffbind CPM TMM

updated 4.1 years ago • shangguandong1996

fine. For some purpose, I needed to redo everything using the hg19 version of the genome. At the DiffBind step, the same script that did not have any problems before had only one error when dealing with the Y vs H comparison...DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length at the point of my script that I was doing a volcano...more. **The concrete pro…

diffbind

updated 4.9 years ago • melnuesch

to test for differential binding above a log2 fold change threshold in the dba.analyze() portion of DiffBind? I understand we could use the fold argument in dba.report() to extract the subset of results that meet the desired...in dba.analyze() to obtain results from all routines. If thresholded testing is not possible in DiffBind, I could try to just export the relevant objects and perform the te…

diffbind

updated 7.9 years ago • le2336

Hi i would like to get help to export my data from diffbind into ChIPPeakAnno for annotation I tried dba.report(DBA, contrast=1, bNormalized=TRUE,bCalled=FALSE, bCounts=FALSE

chippeakanno diffbind

updated 9.5 years ago • joydeepbhadury

Hi, Rory, When I read the DiffBind tutorial I saw that the input is a CSV file that contains sample information. For the Peaks column I think the peaks...I just use one BAM file (either patient or control) to call peaks for the samples, can I still use DiffBind to do the differential analysis? I am new here, if the DiffBind can do it I will try to find out how, but if not I need to switch

DiffBind

updated 2.6 years ago • Huanhuan

I was wondering whether there was a way to take DESeq2 results and convert these to a DiffBind object for downstream processing? Thanks

deseq2 diffbind

updated 5.5 years ago • rbronste

I have chip-seq data which I am analysing with Diffbind. I understood the "blocking factor" functionality of it can be used to remove confounding variables. In the Diffbind...I have chip-seq data which I am analysing with Diffbind. I understood the "blocking factor" functionality of it can be used to remove confounding variables. In the Diffbind manual, the confounding factors used as examples ar…

diffbind chip-seq

updated 4.5 years ago • melnuesch

I am using DiffBind to find the overlapped peaks. I used the following commands: mcf <- dba.peakset(mcf,peaks=peaks.v,peak.caller=peak.caller.v...wrong with my command.  I am justing wondering how the overlap between peaks are calcuated in DiffBind. Thank you, Aimin &nbsp

diffbind

updated 6.8 years ago • aimin.at.work

Hello! TIA for helping =) so via DiffBind, I import a SampleSheet: ```SS <- DiffBind::dba(sampleSheet = csvFile, scoreCol = 5)``` The sample sheet has 6 bed files, 3 replicates...of one sample and 3 replicates of a second sample. I made the venn diagram: ```Venn <- DiffBind::dba.plotVenn(SS, 1:3)``` everything works great and I get the number of peaks that overlap between th…

chipseq DiffBind

updated 18 months ago • Nicole

Currently I'm running DiffBind using bam/bed files that have been filtered to keep only the highly reproducible peaks (HR-peaks), obtained using...However, in a discussion with my colleagues a point was raised mentioning that the input for DiffBind should be all peaks on the dataset and not only the HR ones, resulting in way less DB peaks for some of our marks/conditions...I find this a little bi…

DiffBind

updated 12 months ago • Oscar

Hi everybody, right now Iam trying to analyse my MeDip data set using Diffbind and Iam quite confused whather to use edgeR or DESeq2 for the analysis (iam a biologist with zero training in statistics

diffbind medip-seq edger deseq2

updated 6.5 years ago • florian.noack

The peak format required by DiffBind is BED, whereas MACS2 does not output BED files as MACS14 (the earlier release) did. Rather, it outputs BedGraph (bdg...The peak format required by DiffBind is BED, whereas MACS2 does not output BED files as MACS14 (the earlier release) did. Rather, it outputs BedGraph (bdg) files

chip-seq peak calling diffbind

updated 4.9 years ago • aviv.de-morgan

Hi all, I have used DiffBind to come up with some differentially bound/occupied sites in chromatin accessibility data and for some downstream

diffbind differential binding analysis

updated 7.2 years ago • rbronste

Hi to all, Simple question for DiffBind that isn't clear to me despite a lot of searching and (over) thinking. How exactly is the count data treated when one...Hi to all, Simple question for DiffBind that isn't clear to me despite a lot of searching and (over) thinking. How exactly is the count data treated when one invokes...or would you recommend TMM / RPKM required in addition (or instead …

diffbind chip-seq normalization deseq2 tmm

updated 7.3 years ago • siklenkak

set num cores and how many reads to store in memory diffbind$config$cores <- db_config$cores-1 diffbind$config$yieldSize <- 20000000 # get counts diffbind$config$scanbamparam...FALSE, hasUnmappedMate=FALSE, isMinusStrand=NA, isMateMinusStrand=NA)) # get counts diffbind <- dba.count(diffbind, summits=DB_summits, bUseSummarizeOverlaps = TRUE, bParallel = TRUE) pr…

DiffBind

updated 6 weeks ago • red_bricks

Hi, I have tried to install DiffBind under R3.5.1 (Rstudio), but I cannot as the dependency amap requires R3.6. Is this a known problem? Is there a work around...for using R3.5? Error msg installing DiffBind: >BiocManager::install("DiffBind") ... ERROR: dependency ‘amap’ is not available for package ‘DiffBind’ ... Error msg installing

DiffBind ama

updated 3.8 years ago • Ian

Hi, I\`m trying to use DiffBind package and having an error with __dba__ command: cannot allocate vector of size 2GB. I\`m running the most recent...DiffBind version, 64-bit version of R on a computer with 8GB RAM. I reduced the number of samples from 6 to 4, but still get the same

R diffbind

updated 6.7 years ago • ekgush

cell lines as well as the DBs that are unique to each cell line. I have tried the blocking factor in diffbind, and got two lists of DBs from analysis with and without blocking factor. Is there built-in functions in Diffbind for

diffbind differential binding analysis blocking

updated 6.3 years ago • zhangly811

span style="line-height:1.6">This is a question on the dba.report function of DiffBind. I'm trying to retrieve only the upregulated differential sites and have been using the "bUP" and "fold" arguments...span style="line-height:1.6">  I'm using R 3.0.2 and DiffBind 1.8.5 I'd appreciate any help on this. …

diffbind

updated 9.4 years ago • meisan406

I would like to know how to format the macs2 peaks to be used in diffbind package. I have the following files: <code>omodel_model.r omodel_peaks.broadPeak omodel_peaks.gappedPeak

diffbind macs2

updated 8.4 years ago • tony

Hello, I have been working with DiffBind for 6 months.  When I updated DiffBind 2.6.1 last week I got some warnings. I don't understand what's wrong. I used...nbsp; R CMD INSTALL DiffBind\_2.6.1.tar.gz. same as I installed DiffBind 2.4.8 Warning messages: 1: no function found corresponding to methods...Ontologyâ when loading âAnnotationForgeâ Then previously worked scrip…

diffbind atac-seq dba.count

updated 6.4 years ago • zhaolin20042008

question, but I would like to remove the background color (gray shade) from the volcano plot of Diffbind result : dba.plotVolcano(db) Any comments or suggestions would be greatly appreciated. Thank you

diffbind

updated 4.1 years ago • hy

hey everyone, I'm performing ChIP-Seq analysis using diffbind, after doing: > dba.count(peaksets, summits=250) I would like to get the binding affinity Matrix into a text file. help

diffbind dba.count

updated 5.2 years ago • hamaor

I was wondering how Diffbind deals with the problem of using multiple blocking factors (let's say, age, gender and postmortem delay). If there is...I was wondering how Diffbind deals with the problem of using multiple blocking factors (let's say, age, gender and postmortem delay). If there is a...at the same time, what's the best way of doing it? Should I correct this manually myself somehow, or …

diffbind block regression deseq2 chipseq

updated 3.5 years ago • melnuesch

MACS2 considering matched inputs. To perform the differential binding analysis, I finally ran the DiffBind package on those data. When I created the DiffBind dba object with : <pre> Expe_K4Me1 <- dba(sampleSheet=Samples_K4Me1...biological replicates. Here is an example for K4Me1, showing the correlation heatmap reported by DiffBind when creating the dba object (D0K4Me1\_…

diffbind

updated 8.9 years ago • Pierre-François Roux

Hello! I met a problem when I tried to construct DBA object with dab() in Diffbind. This is my sampleSheet. ![enter image description here][1] And the command dbaNSD <- dba(sampleSheet="sampleSheet.csv...Hello! I met a problem when I tried to construct DBA object with dab() in Diffbind. This is my sampleSheet. ![enter image description here][1] And the command dbaNSD &l…

DiffBind

updated 3.4 years ago • ahua217