Hi there,
I am trying to use diffBind to obtain a set of consensus peaks and fold changes for three different transcription factors chipped. I am comparing...vs. mut, with one gene knocked out in mutant. For one of the transcription factors, I only have one replicate as the second replicate has failed. As a result, I am getting errors from diffBind. Any advice on how to proceed? Thank
Order by: Relevance
Hi,
I am finding the differential peaks using DiffBind, but my sample has no replicates. And my `SampleSheet` is
```
> dbObj <- dba(sampleSheet="SampleSheet.csv")
trisomy_21 fibroblasts...33153 sites in matrix (47495 total):
ID Tissue Factor Condition Treatment Replicate Caller Intervals
1 trisomy_21 fibroblasts trisomy_21 trisomy_21 trisomy_21 1…
updated 6.2 years ago • zhangdengwei
contains two histone modifications (me1 and me2), both mapped in WT and mutant cells. I don't have replicates for any of those. Before I do more replicates, I want to test if there are any significant differential binding 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 yo…
updated 8.2 years ago • Hesh
Hi Rory,
I very well realize the importance of replicates as well as your advice in this forum multiple times to other questions earlier that no meaningful statistics...can be done without replicates.
However, the data I have received to analyze has bad replicates. There are three matched pairs for two conditions...and the biologist says that they can be loosely considered as replicates, b…
running Diffbind, I don't find any significant differential binding sites. However, if I take the intersection of replicates in each...the other.
Those peaks should be statistically significant, but I am not sure I understand why DiffBind did not find any regions that are significant although some regions exist in one group but not the other after taking...the intersection of replicates in eac…
updated 2.9 years ago • narzouni
Hello, I am running Diffbind for Cut&Run data. It is from rare types of tumors that unfortunately was not possible to create replicates. However
updated 4.5 years ago • Danielle
Hello Rory,
Thanks for the Diffbind package, it makes DB analysis very easy.
However, I have the following question: How does DiffBind handle Input samples...A B
IP 2 2
IN 2 2
The number 2 indicates 2 biological replicates for each cell.
When DiffBind calls DESeq2, what contrast does it use internally to calculate LFC and FDR between
updated 6.2 years ago • liruiradiant
<div class="preformatted">Hi all,
I am trying to use DiffBind to compare peaks called in control vs
condition. I have 2 replicates for each and I've also called peaks
using 2
different peak callers (to wi, MACS and QuEST). I've also prepared a
sample
data sheet that looks like this:
SampleID Tissue Factor Condition Replicate Peak.caller
bamReads
bamControl Peaks
control …
Dear Bioconductor community,
I am interested in using DiffBind. I am following the procedure in "DiffBind: Differential binding analysis of ChIP-Seq peak data" and I got a bit confused...Dear Bioconductor community,
I am interested in using DiffBind. I am following the procedure in "DiffBind: Differential binding analysis of ChIP-Seq peak data" and I got a bit confused, I hope you can help me.&…
updated 9.1 years ago • omiguele
Hi DiffBind Team,
I've been looking to use your package to analyse some ChIP seq data and have been following the vignette for...My data has no replicates and I'm fully aware that this is not a good study design, but it's the data we have to work with. I have been working with...two peak callers (MACS and SPP) and was hoping to treat these two sets of peaks as "replicates" in DiffBind. I'm convi…
updated 8.3 years ago • Sophie Shaw
all (and hopefully Rory would see this. Thanks for the great program)
I have ChIP-seq data of 3 replicates of wild type and 3 replicates of my mutant.
I'm looking for loci where my protein binds in WT samples (so WT has peaks...has no peaks (the protein doesn't bind to the same loci in the mutants).
I think this is what DiffBind manual explained as Occupancy analysis.
On the page…
updated 3.2 years ago • Junsik
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 …
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...home/labs/shlush/avivdm/chipseq_313_75/9_macs_broad/wt2_ip_chip_7-5.NOMOD_peaks.broadPeak", package = "DiffBind"),
peak.caller = "narrow", sampID="WT2_…
I am trying to compare two different conditions (with 2 replicates each) using Diffbind. For my Diffbind output, I'm getting 0 counts for one of the conditions and high counts for the...to match my normalized browser tracks. There's clearly a peak around the chromosome position, but Diffbind is calculating it as 0 counts. There's definitely still a change in peak intensity between the two conditi…
updated 3.0 years ago • slrpatty
div class="preformatted">Hi Robin-
The HOMER peak format is not supported natively by DiffBind. You'll
need to convert the peak file format to a supported one -- the easiest
is the default ("raw") which has four columns...the
first 40 lines of header as well.
I should mention as well that with only two peaksets and no
replicates, you can not really perform a meaningful differential
analysis …
gt;
Cc: Daniele Merico
<daniele.merico@sickkids.ca<mailto:daniele.merico@sickkids.ca>>
Subject: Diffbind : use of controlBam
Dear Rory Stark ,
we used DiffBind with MACS peaks.
In our experiment, we had 3 biological replicates...ctrl vs rep2-tumorand rep3-ctrl vs
rep3-tumor . This gave us the peaks for each control and tumor
replicate. This is approved by the MACS protocol.
Wh…
I am using Diffbind to compare H3K27ac peaks between two time points. Recently, we added 4 more time points to the existing 2 to do time...series comparison.
From my understanding, Diffbind could conventionally compare and provide differential bound sites between 2 samples .
Q1: Is there a way to compare...and contrast 6 time-points, considering each has 2 biological replicates.
Q2 If the an…
Hi,
I have been using DiffBind to perform differential binding analysis on ChIP-seq data, comparing two groups with 3 replicates for each. I am now...any error message. In addition, this error message did not appear, when I used an older version of DiffBind. This error happens after I have updated R to ver. 3.3.1 and downloaded the latest version of DiffBind.
Thank you
updated 9.5 years ago • shohei.hori
for that peak. The second "count" heatmap gives a much
less biased view of how samples, including replicates, are correlated,
as it takes into account the read density at every site in every
sample.
If your replicates cluster...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 DiffB…
2036_K4_peaks.xls", package="DiffBind"),
peak.caller="macs", sampID="WT2036",tissue="BM B cells",
factor="WT",replicate=2)
dp.K4 <- dba.peakset(dp.K4,
peaks=system.file...1945_K4_peaks.xls", package="DiffBind"),
peak.caller="macs", sampID="WT1945",tissue="BM B cells",
factor="W…
is that someone can help explain why I might be getting results like these, and how I might tweak DiffBind's parameters to get better results, or if I'm not understanding how DiffBind is intended to work in the first place...I chose minOverlap of 2 for dba.count(), but I am unsure if this means the peak must show up in both replicates for a given condition, or two out of any of the peak files. I …
you could clarify for me.
So in my chip-seq experiment, I have 2 conditions (2 biological replicates for each). Whenever I visualize the peaks in IGV or plot the MACS2 output bed scores in R, I see that overall, all counts...to the other.
However, whenever I compare counts from the consensus peakset generated by DiffBind, the dramatic difference is gone.
I don't exactly understa…
updated 10.7 years ago • mm2489
I'm trying to load in peaksets from a BED file (the summits output from macs2 callpeaks), and I'm running into an error
Here's what the first line of my BED file looks like:
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-G…
Hello,
I'm using DiffBind to extract peaks that appear in my replicates. I have four replicates, and I wish to fetch peaks that are in at least...3 replicates. It doesn't matter which 3/4 (or 4/4) replicates they appear in. How do I achieve this? I expect it has to do with minOverlap
updated 4.0 years ago • Krista
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...TRUE,minOverlap = 1)</em></pre>
I had a surprisingly low correlation (< 0.2) between biological replicates. Here is an exampl…
updated 10.6 years ago • Pierre-François Roux
I have 10 "summit" bed files from macs2 peak-calling, with 5 factors with 2 replicates each.
I added them all one-by-one to a dba object "dbObj" that looks like this:
10 Samples, 3202 sites in matrix (234027...I have 10 "summit" bed files from macs2 peak-calling, with 5 factors with 2 replicates each.
I added them all one-by-one to a dba object "dbObj" that looks like this:
10…
Hi, I have a set of data (cut and run) with 2 samples, three replicate of each. One set of replicate are separated from the other two replicates in sample heat map while the other two set...of replicates are segregated by sample (treatment replicate 1 next treatment replicate 2 and control 1 next to control 2). My question...is how do I go about to use mask to create a dba object just containi…
updated 15 months ago • Haiping
and Lactose (Induction condition)
3 epigenetic marks : H3K4me3, H3K9me3 and H3K27me3
3 replicates for each mark and each condition
2 inputs for each condition
1 mock for each condition
The three replicates for...each condition are biological replicates from which I IPed my three marks :
Glucose condition :
Biological replicate 1 : H3K4me3 (1) H3K9me3 (1) H3K27me3 (1) Input...1)
Biologica…
updated 4.9 years ago • SFn
Hi,</p>
<p style="direction: ltr;">I'm trying to analyze chip-seq histone modification data with diffBind. When I try running diffBind, it tells me that my bam files cannot be accessed. It was able to make the plot based on the...file):</p>
<div style="direction: ltr;"><span style="line-height:1.6">SampleID, Condition, Replicate, bamReads, ControlID, ba…
Hi,
I'm using DiffBind to analyze a set of ChIP sequencing data. For each sample, I have three biological replicates. I performed the ChIP...SICER. Now I'm interested in performing an overlapping analysis using the three biological replicates. In the SICER output there is an enrichment value for each peak (this means an enrichment respect to the input). Is
updated 11.0 years ago • robertacar
div class="preformatted">Dear All,
I am trying to use DiffBind and having an error. The data set is just
two conditions without any replicates. I set up the contrast manually
as groups...operator is invalid for atomic vectors
In addition: Warning messages:
1: Some groups have no replicates. Results may be unreliable.
2: In estimateCommonDisp(res) :
There is no replication, setting dispersio…
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...count data.…
updated 10.0 years ago • surjray
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...Replicate,bamReads,bamControl,Peaks,PeakCal
ler
>NE_1,Testis,Normal,1,NE_HILSI_1.bam.bed,NE_HILS_1_Input_peaks.bed...bed
…
updated 12.2 years ago • Rory Stark
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…
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",…
Hi Dr. Stark,
I was wondering if I could ask for your assistance with something DiffBind related please? My ChIP-seq experiment consists of five treatment groups (negative control, drug 1, drug 2, drug 3, drug...4) with two replicates per sample (i.e I have 10 .bam files in total, and 10 .narrowpeak files). Unfortunately, I do not have access to a high...computing cluster so am using the lates…
updated 2.8 years ago • epipally
Hello Dear community,
I am trying to apply DiffBInd package to perform a binding analysis of two TFs from the same family, TF1 and TF2. My goal is to understand to what...Hello Dear community,
I am trying to apply DiffBInd package to perform a binding analysis of two TFs from the same family, TF1 and TF2. My goal is to understand to what extend these two TFs act cooperatively so we have ChI…
score and see how it compares
to
RPKM_FOLD.
Also, from the labels I think perhaps you have combines replicates of
specific factors/marks? You may want to break them out so you have
replicates of each ChIP, if only as a control...2013 16:46:38 -0400
To: Rory Stark <rory.stark at="" cruk.cam.ac.uk="">
Subject: Re: DiffBind questions
Hi Dr. Stark,
I've been using DiffBind for my analysis …
updated 12.4 years ago • Rory Stark
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...nbsp; factor=factor.v,condition=condition.v,replicate=replicate.v)
dba.plotVenn(mcf,mask=c(17,19),main=paste0(colnames(mcf$class)\[c(17,19)\],collapse = “-…
updated 8.5 years ago • aimin.at.work
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
updated 11.4 years ago • enricoferrero
Is it possible to run diffbind with my "own" binding affinity table? I might want to delete certain peaks or have my own way of combining peaks across...replicates.
Let's say I have a table `mytable.tsv` that looks like this:
sample1 sample2 sample3
peak1 312 366 12
peak2 999 12 512
Hi 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
Is there a limit for the sequence coverage difference between replicates and among samples?
I am using DESeq2 and edgeR in DiffBind to compare ATAC-seq samples with different sequencing...Is there a limit for the sequence coverage difference between replicates and among samples?
I am using DESeq2 and edgeR in DiffBind to compare ATAC-seq samples with different sequencing coverage among samples,…
IDR method (for reference: https://hbctraining.github.io/Intro-to-ChIPseq/lessons/07_handling-replicates-idr.html), obtaining a good amount of DB peaks.
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…
updated 2.8 years ago • Oscar
div class="preformatted">Hi
I have been trying to use DiffBind to analyze our Chip-seq data and
have
been running into some errors repeatedly.
I first created a samplesheet.csv...describing my samples and it looks
like this:
SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks,P
eakCaller
meio.1,meiocytes,H3K4me3,N,1,M_meiocytes_H3K4me3.bam,InM_input_meiocyt...each
and the …
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...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-seq data. I have 7 different cell types with 1-3 …
updated 7.2 years ago • duvaller
could you point it out to me so I can fix it?
3. In the case of plotting peaks (without counts), DiffBind first
merges all the overlapping peaks to form a master peak list. To
construct the vector for each peakset, it assigns...e.g. a
promoter), you may want to take a look at the MMDiff package -- you
can use your existing DiffBind objects in MMDiff.
4. Currently DiffBind will merge together an…
Hi bioconductor team,
I'm analyzing atac-seq data with 4 genotypes and two biological replicate for each of them (8 samples overall). 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 an…
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…
updated 13.0 years ago • Rory Stark
I am currently working on an analysis of two factors with two replicates each. I have called peaks using three different peaks callers, and would like to first derive a consensus of the...without having to create multiple DBA's?
My current workflow is:
- create DBA with ALL samples, replicates and peak calls (2 x 2 x 3 = 12)
- generate consensus for each factor
- export and save consensus…
updated 6.0 years ago • Jim
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)  ...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…
Hello,
I'm new to DiffBind and have 3 tissues with 2 replicates each. I have been able to generate plots with contrast 1-3 to compare each pair
updated 5.1 years ago • Divya
div class="preformatted">Hi again,
I am trying DiffBind and loaded my data that looks like this:
H3K4m3
4 Samples, 13203 sites in matrix (13792 total):
ID Tissue Factor Condition...Peak.caller Replicate Intervals
1 wt1 Hela H3K4me3 control1 raw 1 14111
2 wt2 Hela H3K4me3 control2 raw 2 13771
3 treat1 Hela H3K4me3...de Jesus Domingu…
I'm currently using esATAC to process a number of ATAC-Seq samples that are done in two biological replicates across four sample groups. I'm interested in using DiffBind to calculate read counts from the resulting *PeakCallingFseq.bed...in a dba sample sheet:
- SampleID: a unique ID that is composed of the content from Factor and Replicate columns (8 samples)
- Factor: A combination of conten…
Hi,
I want to use DiffBind for differential accessible chromatin regions for my ATACSeq analysis. I am trying to understand the core codes...for this analysis as described in DiffBind manual but getting bit confused due to many interlinked options. If the metadata (information of case, control, replicates...with the command "dba.analyze("File.csv")". With this scenario I have three questions:
…
updated 2.9 years ago • tahir.msajid
Hi,
I have peak file for four different condition without replicate. I converted the text file to Bed file by taking column 2,3,4,8 and 5 which is chr, start, end, score and strand respectively...Hi,
I have peak file for four different condition without replicate. I converted the text file to Bed file by taking column 2,3,4,8 and 5 which is chr, start, end, score and strand respectively and als…
updated 10.5 years ago • Gyan Prakash Mishra
Hello forum
I am trying to conduct a H3K27ac ChIP-seq analysis in Diffbind version 3.16 in R, but every time i try using dba.count to generate the count matrix, I "lose" peak regions due to default...Hello forum
I am trying to conduct a H3K27ac ChIP-seq analysis in Diffbind version 3.16 in R, but every time i try using dba.count to generate the count matrix, I "lose" peak regions due to d…
updated 9 months ago • ALL_antla
Dear colleagues,
I'm using DiffBind for the first time and I'm encountering some issues, one in particular is quite weird.
I've got a simple experiment...Dear colleagues,
I'm using DiffBind for the first time and I'm encountering some issues, one in particular is quite weird.
I've got a simple experiment, 3...conditions, 4 replicates each.
I've obtained peaks using MACS2 (-- broad fu…
updated 17 months ago • Marianna
each factor might have different frip, and it can cause biases in the comparisons.
Is it OK to use DiffBind / csaw to compare these two ChIP seq samples (with replicates of course)?
Thanks
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...the problem. Thank you very much in advance for your help.
I have a total of 4 samples,…
updated 10.7 years ago • ruka.setoguchi
Recent ...
Replies
Comment: Pairwise comparison of multiple groups with different base
by
ja569116
•
0
Hi @mikelove
I have a similar situation, and I feel that I have interpreted the results in the wrong way. In my case I would like to identi…
Comment: Are individual-mouse-based statistics possible in CellChat?
by
TikTsossakaas33ocissalpc
•
0
Questions about comparing groups and statistical significance highlight how data driven thinking matters across fields. In online mobile ga…
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
•
0
Hi @atpoint Thanks for the information.
Could you please expand on when to use adjusted p-values vs nominal p-values.
My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Awards
• All
Popular Question to
Lluís Revilla Sancho
▴
760
Popular Question to
nromerov
•
0
Popular Question to
Thomas Girke
★
1.7k
Teacher to
Gordon Smyth
53k
Popular Question to
Stephanie M. Gogarten
▴
890
Locations
• All
The city by the bay, 2 minutes ago
Melbourne, Australia, 5 minutes ago
WEHI, Melbourne, Australia, 6 minutes ago
Australia, 26 minutes ago
United States, 27 minutes ago
The city by the bay, 2 minutes ago
Melbourne, Australia, 5 minutes ago
WEHI, Melbourne, Australia, 6 minutes ago
Australia, 26 minutes ago
United States, 27 minutes ago
Traffic: 1100 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6