Bioconductor Forum

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 4.1 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> <em>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 9.5 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 4.0 years ago • ahua217

Hi, I am trying to help a labmate who is using DiffBind to do a PCA analysis on some ATAC-seq data that she generated. I have experience with PCA but not with this specific...Hi, I am trying to help a labmate who is using DiffBind to do a PCA analysis on some ATAC-seq data that she generated. I have experience with PCA but not with this specific software. How can we retrieve the PCA loadings/eige…

DiffBind dba.plotPCA

updated 3.5 years ago • Spendlove

Hello, I am trying to understand DiffBind in order to use it for my ATAC-seq data analysis and find differential open chromatin sites. could you please explain

atac-seq

updated 8.7 years ago • simonjean434

30:49 +0530 To: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Subject: DiffBind Questions Dear Rory, We have been using DiffBind on our Chip-seq data. I would like to know, to see the correlation replications

DiffBind DiffBind

updated 10.8 years ago • Rory Stark

Hi Rory Stark, I am a little confused about the following questions regarding the use of DiffBind: How does DiffBind handle normalization? Does it use the raw counts from BAM files? Are the total reads counts used...as we analyze RNA-seq read counts, which require raw read counts as input? Is it possible to use DiffBind without spike-in normalization? Thanks in advance

DiffBind

updated 21 months ago • skyyks123

paolo 2012/7/31 Gordon Brown <gordon.brown at="" cancer.org.uk="">: > Hi, Paolo, > > DiffBind uses quite a lot of memory for the dba.count step, because it loads > the whole data file into memory. (In hindsight...C:/Documents and Settings/pkunderfranco/Documenti/Data /ChIP-seq >>> Roberto/Analisi_PK/DiffBind/H3K27me3/") >> &am…

Cancer CMA DiffBind Cancer CMA DiffBind

updated 12.3 years ago • Paolo Kunderfranco

How to correct this error `` More fragment sizes than libraries `` in DiffBind Package ? What does that means

diffbind

updated 7.5 years ago • ZheFrench

Enter the body of text here Code should be placed in three backticks as shown below ```#DiffBind version 3.2.4 library(DiffBind) getwd() setwd("/Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC...Screening.csv", header=TRUE, sep=",") names(samples) samples #read peaksets using the "dba" DiffBind function and creates a DBA object #The peak score (prior to counting reads) i…

DiffBind

updated 3.3 years ago • mtsompana

So I am using DiffBind to create a count matrix as summarizedExperiment and then running this through DESeq2 and I was wondering about...So I am using DiffBind to create a count matrix as summarizedExperiment and then running this through DESeq2 and I was wondering about ways to filter for specific baseMean ranges within this data? My script looks like the following: <pre> library("DESeq2…

deseq2 diffbind basemean summarizedexperiment

updated 6.3 years ago • rbronste

Stark <rory.stark@cancer.org.uk<mailto:rory.stark@cancer.org.uk>> Subject: Question concerning Diffbind Resent-From: Rory Stark <rory.stark@cancer.org.uk<mailto:rory.stark@cancer.org.uk>> Dear Dr. Stark I am a graduate...student at POSTECH and have a question concerning DiffBind. I have multiple samples of different condition but do not have any replicate nor co…

Normalization GO edgeR DiffBind Normalization GO edgeR DiffBind

updated 11.8 years ago • Rory Stark

Hi,   I'm using Diffbind to analysis differential binding H3K27Ac histone ChIP-seq site! I'm curious whether I can find all the relative...Hi,   I'm using Diffbind to analysis differential binding H3K27Ac histone ChIP-seq site! I'm curious whether I can find all the relative site

diffbind chipseq histone chip-seq differential binding analysis

updated 6.1 years ago • woongjaej

I have some questions about Diffbind analysis when there are multiple groups to be compared. For example, if we have group1, group2 and group3 and wish...I have some questions about Diffbind analysis when there are multiple groups to be compared. For example, if we have group1, group2 and group3 and wish to

diffbind

updated 4.1 years ago • Vince Schulz

51:49 +0100 To: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Subject: DiffBind and paired end data Dear Dr. Stark, I had the pleasure to attend ("back then in 2013") to the presentation you gave at the...EBI Advanced Course for RNA-seq and ChIP-seq, where you introduced DiffBind and its usage examples. Now I moved from IMB - Mainz and I am working in…

DiffBind DiffBind

updated 10.7 years ago • Rory Stark

Sorry for the mundane question, but I think I used to be able to change the color of heatmaps in Diffbind using col = , and now that doesnt seem to work,  Now I get the following error: > plot(samples\_final, col ="blues") Error

diffbind rory stark

updated 7.3 years ago • andrew.gehrke

Hi folks, I am new to ChIP-seq analysis hence this may be a basic question. I want to use DiffBind to get peak summits, but after running `dba.count` with my own peaks, I find the number of peaks has decreased. Is this...Hi folks, I am new to ChIP-seq analysis hence this may be a basic question. I want to use DiffBind to get peak summits, but after running `dba.count` with my own peaks, I f…

DiffBind

updated 2.7 years ago • soyabean

Hi wondering how I can use the following DESeq2 logic within the framework of DiffBind for calling differential peaks and looking at multiple interactions: <pre> to look at interaction-- dds<-DESeqDataSetFromMatrix

diffbind deseq2 interactions

updated 3.9 years ago • rbronste

Dear Bioconducters I am running ChIPseq analyses via DiffBind 2.2.12 using DESeq option. As indicated in the vignette I run dba.analyze() and the extract the results with dba.report

deseq2 diffbind chipseq

updated 6.5 years ago • rafael.munoz.viana

p style="direction: ltr;">Hi,</p> <p style="direction: ltr;">We are trying to use diffBind and are puzzled by the scale on our correlation matrices. In one of our datasets the correlation goes between 0.9

diffbind scale correlation matrix

updated 9.0 years ago • eli7javasky

Hello! I am performing a differential analysis on ATAC-seq data in DiffBind. I would like to know if it is possible to plot ellipses around a PCA plot. I generated my plots with the following code

PrincipalComponent DiffBind

updated 2.4 years ago • Lisa

Hello, I tried DiffBind (v3.0.9) to find DE binding sites from ChIP-seq data. When I used "dba.normalize" with "background=TRUE". It ended up with...Hello, I tried DiffBind (v3.0.9) to find DE binding sites from ChIP-seq data. When I used "dba.normalize" with "background=TRUE". It ended up with this error: ```r DB = dba.normalize(DB, normalize=DBA_NORM_NATIVE, background=TRUE) Gene…

BiocParallel DiffBind parallel

updated 3.9 years ago • Victor

div class="preformatted">Hi, I'm Ken Tanaka. I'm currently interested in analyzing the DiffBind analysis by using the ChIP-seq data from Th2 immune cell samples. To be more specific, I would like to analyze this...GSE28292) by using DiffBind analysis. I have questions regarding the dba.count(). When I execute the dba.count(), it crashes. The bed data which I...from the problems regarding t…

DiffBind DiffBind

updated 11.5 years ago • kentanaka@chiba-u.jp

mask=1:29, label = DBA_CONDITION, labelSize = 0.65, contrast = 19) Being very new to Diffbind, I would really appreciate if someone could confirm that it is correct. Also, if my code is correct, could someone provide

diffbind

updated 5.7 years ago • Helene

Dear all, is there any way to change the dimension of the PCA plot is the DiffBind package? How can I change label size in this plot? Thanks

Diffbind

updated 4.9 years ago • bony.dekumar

Hi everyone, I am trying to use DiffBind to process an unusually large dataset (101 ATAC-seq samples). Is there a way to construct the dba object using `dba()` in

DiffBind

updated 18 months ago • Shashank

nbsp; Hello, I was looking at previous posts about MACS2 peak files and read shift before DiffBind to match MACS2 settings. However, I am still a bit confused about right steps to take. This is my work strategy: 1) &nbsp...shift 25b from 3' ->5' and after that set read length = 50) 2)  Load NarrowPeaks files in DiffBind and obtain consensus peakset (for all replicates from…

diffbind macs2

updated 6.6 years ago • Lauma R

data similar to ChIP-Seq) after degradation of my protein of interest. I am currently using Diffbind in combination with DESeq2 method of dba.analzye() but diffbind provides so many different options for dba.normalize...when using Option 1 vs Option 2 in dba.normalize(). Thank you! ```r #Importing the the table for diffbind containing all the necessary files, names, and locations CTCF_narrowp…

GenomicLocalization DESeq2 Cut&Run Diffbind Normalization

updated 3.9 years ago • Monica

Hi Rory Stark， DiffBind normalization based on the total reads of a bam file by default, right? And the final results of DiffBind: Conc_Resistant

DiffBind

updated 21 months ago • skyyks123

Would you please help? Thank you so much! https://bioconductor.org/packages/devel/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf Page 22 the manual explains this plot but I am still not sure. ![enter image description here

DiffBind

updated 18 months ago • Chris

Hi , I am currently working on 12 ATAC-Seq samples using Diffbind. Following the tutorial, the first step involved generating a dba object and setting the minoverlap parameter...Hi , I am currently working on 12 ATAC-Seq samples using Diffbind. Following the tutorial, the first step involved generating a dba object and setting the minoverlap parameter to...A, but when I go back to check the input…

diffbind DiffBind

updated 19 months ago • hfyuan2016

Hi, I was trying to use DiffBind to analyze my ATAC-Seq data. When I call the dba.count() function, I got the following error message: Error: Error processing...errors in user code 2:   "croi\_count\_reads" not resolved from current namespace (DiffBind)  3:   "croi\_count\_reads" not resolved from current namespace (DiffBind)  4:&am…

dba.count atac-seq diffbind

updated 7.0 years ago • ew152

I am using diffbind to find differential peaks between different samples obtained in different conditions. The manual says that...I am using diffbind to find differential peaks between different samples obtained in different conditions. The manual says that dba.analyze

diffbind differential gene expression

updated 8.1 years ago • onkarnath89

my hair out trying to figure out how to resolve an issue I am having with reading peaksets into Diffbind. The peaks files I am trying to use are .narrowPeak files derived from MACS2. It is my understanding that Diffbind is...binary operator" ``` I have no "scoreCol" column in my sample sheet. I wondered whether maybe Diffbind was having trouble with the .narowPeak files so substituted thes…

DiffBind

updated 20 months ago • os306

DiffBind"), peak.caller="macs", sampID="WT2017",tissue="BM B cells", factor="WT", replicate=1) dp.K4 <- dba.peakset(dp.K4, peaks=system.file...2036_K4_peaks.xls", package="DiffBind"), peak.caller="macs", sampID="WT2036",tissue="BM B cells", factor="WT",replicate=2) dp.K4 <- …

diffbind macs2 chip-seq

updated 7.0 years ago • chunhong.liu07

9.263 . 9.263 1.709270e+00 2.493753e-02 0 >--------------- > >When DiffBind tries to normalise the score based on the width of the peak, >it comes out as N/0, which R shows as infinity. Things go...downhill from >there. This is a bug in DiffBind (if the width is zero, we should just >make it 1, for example). But in the meantime, to work a…

GO DiffBind NarrowPeaks GO DiffBind NarrowPeaks

updated 10.8 years ago • Rory Stark

to extract such data for specific windows at some point in the analysis. I am asking as I never used DiffBind before and I do not know at which point such control samples are used in the analysis. Thanks in advance

DiffBind chipseq BasicWorkflow

updated 18 months ago • agata17

again, sorry lots of questions at the moment, I would like to replicate the following function from diffBind <pre> > dba.plotMA(tamoxifen, bXY=TRUE) </pre> However I don't know how to retrieve this data, in Deseq2 I believe it would

diffbind ggplot2 r chipseq

updated 7.2 years ago • reubenmcgregor88

Dear DiffBind developers/users, I have runned my histone ChIP-seq differential analysis using DiffBind some months ago. Back then...Dear DiffBind developers/users, I have runned my histone ChIP-seq differential analysis using DiffBind some months ago. Back then I saved my output from **dba.analyze(test_contrast, method=DBA_ALL_METHODS)** as an **.RDS file**. At that point I also used DiffBi…

DiffBind

updated 15 months ago • M.Vukic

<div class="preformatted">Dear list, --I'm trying to use Diffbind package to analyze some samples from a ChIP seq experiment. --I created a .csv samplesheet with the following fields and which samples to analyze: SampleID Tissue Factor Condition Replicate Reads Control Peaks Chip_K27.1+ Neural K27 Responsive 1 Chip_K27.BED Input_K.BED Chip_K27.BED Chip_K27.2+ Neural K27 Responsiv…

DiffBind DiffBind

updated 11.9 years ago • José Luis Lavín

I got a strange PCA (for DiffBind version 2.12.0 which is not the newest version). The first PC explains 90% of the variance. Nevertheless, the distances...which explains a much larger percentage of variance). How to make sense of it? ```r library(DiffBind) design_i <- read.csv("design_vs_Input.csv") dbObj_i <- dba(sampleSheet = design_i) dbObj_i <- dba.count…

DiffBind

updated 3.9 years ago • Sam

DiffBind is wonderful that can cluster my H3K27ac ChIP-Seq samples very well as below fig1. However, is there any method or other

diffbind

updated 9.4 years ago • Gary

Hi all, diffbind takes bam files to calculate the coverage (of course it can be used without setting bam files). Since I would like to

diffbind chip-seq chip spike spike-ins

updated 4.5 years ago • theodore.georgomanolis

this and make the unzipped directory your current directory, instead of system.file("extra", package="DiffBind"), the vognette should run, including the call to dba.count. Cheers- Rory On 20/08/2013 17:46, "Beh Ching Yew" <behchingyew...at="" gmail.com=""> wrote: >Dear Rory, > >I am currently looking into DiffBind for my Chip-Seq data analysis. >Would apprecia…

DiffBind DiffBind

updated 11.3 years ago • Rory Stark

Hello, This question is in regards to using DiffBind (or DESeq2) with multiple samples. Currently, I am using DiffBind (version 2.8.0) to find differential peaks from ATAC

diffbind atac-seq differential analysis deseq2

updated 6.1 years ago • duvaller

Hello all, I am trying to use DiffBind on my ATAC seq data. However, the code in the manual uses ChIP seq data. Would you advise me on what to do for a learner...Hello all, I am trying to use DiffBind on my ATAC seq data. However, the code in the manual uses ChIP seq data. Would you advise me on what to do for a learner? Thank

ATACSeq

updated 20 months ago • Chris

It seems DiffBind run everything on top of dba objects. But all peak data are stored as GRanges objects in my workflow. How to make the

diffbind

updated 8.3 years ago • xulong.wang

Hi, I'm having an issue during the 'Counting reads' and 'Performing the differential analysis' step. I am receiving these messages/errors: ## Performing the differential analysis # .... [TRUNCATED] Warning message: In data(Condition_counts) : data set ‘Condition_counts’ not found OR ## Performing the differential analysis ## > Condition <- dba.ana…

diffbind differential analysis genetics #chip-seq

updated 5.7 years ago • ryclb22

<div class="preformatted">Hi Anna- Before running DESeq, DiffBind sets all counts to a minimum value of 1. Not sure if that is in the documentation anywhere! Cheers- Rory On 11/09/2013 17:47, "Anna Poetsch" <anna.poetsch at="" cancer.org.uk=""> wrote: >Dear Rory, > >I attended the class about ChIP-Seq data analysis at EBI recently, where >you introduced…

Cancer DESeq DiffBind Cancer DESeq DiffBind

updated 11.2 years ago • Rory Stark

<div class="preformatted">Hi Rong- You are correct that the peak merging logic results in wider peak areas that may incorporate multiple binding sites and/or make it more difficult to determine the precise binding site. This is true of the peak calling step as well. In our experience, the scientific questions we are actually asking do not require the precise binding location in the differe…

DiffBind DiffBind

updated 10.5 years ago • Rory Stark

52, "Goutham atla" <goutham.atla at="" gmail.com=""> wrote: >Dear Dr. Stark, > >I am using DiffBind for Chip-Seq data analysis. I have biological >replicates between two conditions. > > >SampleID,Tissue,Condition...and Conditions ), should I perform any >normalization of the data ( MANorm etc ) ? Or The DiffBind will take >care…

Normalization DESeq DiffBind Normalization DESeq DiffBind

updated 11.0 years ago • Rory Stark

I have a question about the DiffBind program. I am an immunologist and have recently started to use R for data analysis. Now, I am trying to analyze our ChIP...seq data using DiffBind to identify genomic regions that are commonly or differentially bound by one transcription factor and its mutant...nbsp; I have a total of 4 samples, two replicates for each condition. I used R: 3.1.3 version and …

diffbind

updated 9.6 years ago • ruka.setoguchi

events between WT and mutant cells for both histone modifications. Can I analyze this data using DiffBind even though I don't have replicates?    Thank you!&nbsp

diffbind bioconductor differential binding analysis without replicate chipseq

updated 7.0 years ago • Hesh

to clarify some technical details which I’ve been trying to search for in the documentations for DiffBind, but seem to have missed it. I am interested to know the details of how the correlation of occupancy (using peak caller

diffbind duplicatecorrelation

updated 10.0 years ago • meisan406

Is there a way to grep the percentages PC1 and PC2 variance explained from dba.plotPCA in diffbind or chipQC ? In my pca plot PC1 and PC2 numbers seem inversed . I'd like a way to recompute them from scratch (as asked&nbsp

diffbind chipqc

updated 7.2 years ago • ZheFrench

DiffBind 2.2.12. I guess that it is because my DiffBind is not the last version, i.e. 2.4.8. However, when I install DiffBind again...for an HTML browser interface to help. Type 'q()' to quit R. > require("DiffBind") Loading required package: DiffBind Loading required package: GenomicRanges Loading required package: stats4...found in "…

diffbind

updated 7.2 years ago • Gary

Hi, I have been working with Diffbind to identify differential binding of H3K9me3 due to ethanol treatment. We are using both males and females, and initially

DiffBind multifactoranalysis

updated 8 months ago • erbrocato

<div class="preformatted">Hi, Is there a way to use DiffBind to analyse time course data? I have sample and control replicates at five different time points and I would like to...div class="preformatted">Hi, Is there a way to use DiffBind to analyse time course data? I have sample and control replicates at five different time points and I would like

DiffBind

updated 10.2 years ago • enricoferrero

As part of the latest Bioconductor release 3.12, `DiffBind 3.0` includes extensive updates of which users should be aware. The purpose of these updates, reflecting user comments...incorporating up-to-date methods and utilizing knowledge and experience gained in the 10 years since `DiffBind` was first written. The main updates are in the areas of **modelling**, **analysis**, **normalization**, …

Normalization ATACSeq ChIPSeq DiffBind chipseq

updated 3.9 years ago • Rory Stark

<div class="preformatted">Hi, Your sample sheet shows the same filename for "Reads" and "Peaks", which is unlikely to be right. The "Peaks" file should be the output of the peak caller (the peaks that MACS called); the "Reads" file should be the aligned reads, i.e. the *input* to the peak caller (the output of the alignment stage). Let me know if that fixes the problem. It should give a…

DiffBind DiffBind

updated 11.9 years ago • Gord Brown