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
Order by: Relevance
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
updated 9.8 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 …
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
 
updated 9.5 years ago • mm2489
Hi community!
I am providing to Diffbind a genomic region list to be analyzed (not peaks, just regions of interest). Although the results are good, I want to avoid...Diffbind to merge some of the regions that actually overlap. Can I do that? I have trying so far with no success. Any help?
Thanks
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…
updated 8.8 years ago • surjray
Dear all,
I'm using DiffBind to find the differentially methylated regions.
Libraries have been obtained by using the Methyl-binding domain...suggestions to deal with ATAC-seq but not with MBD-seq.
I wonder if someone has experience with DiffBind and MBD-seq.
Should I go for the background or the Reads in Peak (RiP) normalization? Are there some specific "rules" for
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
updated 3.5 years ago • joseluis.ruiz
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…
updated 3.7 years ago • Lucky
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 …
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="/…
updated 7 months ago • Virangika
Hi,
Can I use HOMER called peaks in DiffBind without making any changes to the peaks file (HOMER output file)?
Thank you
 
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
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
 
updated 8.0 years ago • rebecca.spokony
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…
span style="line-height:1.6">Hello,</span>
<span style="line-height:1.6">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 </span>analyse<span style="line-height:1.6"> the data in DiffBind. I saw that I can introduce a column in the csv t…
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…
updated 4.7 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
updated 14 months ago • zgyu12
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
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
updated 8.2 years ago • igor
In the `DiffBind` package, how can I extract the t-statistic from the `dba.report
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…
updated 6.3 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…
updated 9.3 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",…
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 ...normal distribution. Does DiffBind use a non-parametric method? Or DiffBind use scores (e.g. FDR value) for …
updated 4.1 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
updated 4.0 years ago • C T
Hello!
Is it possible to plot principal components 3 and 4 with Diffbind plotPCA function? - thanks
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…
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…
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 <
updated 6.5 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…
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, …
updated 2.1 years 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…
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
updated 3.6 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…
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
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…
updated 8.5 years ago • le2336
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…
updated 5.5 years ago • melnuesch
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
updated 10.1 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
updated 3.2 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
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…
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  
updated 7.4 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…
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
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…
updated 19 months ago • Oscar
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
updated 5.5 years ago • aviv.de-morgan
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...cooperatively so we have ChIP-seq data of bo…
Hi all,
I have used DiffBind to come up with some differentially bound/occupied sites in chromatin accessibility data and for some downstream
updated 7.8 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 …
updated 7.8 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…
updated 8 months 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
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
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
updated 6.8 years ago • zhangly811
span style="line-height:1.6">This is a question on the dba.report function of DiffBind.</span>
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"> </span>
<span style="line-height:1.6">I'm using R 3.0.2 and DiffBind 1.8.5</span>
I'd appreciate any help on this.
…
updated 10.0 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<br/>
omodel_peaks.broadPeak<br/>
omodel_peaks.gappedPeak
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…
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
updated 4.7 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
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 …
updated 4.0 years ago • melnuesch
Recent ...
Replies
Comment: Identical samples after deseq2 batch effect removal
by
Michael Love
42k
I'm adding my comment to the threaded section ...
I don't have any suggestions here but whatever method you're using is not appropriate up…
Comment: ANOVA like approach of edgeR
by
Yunshun Chen
▴
870
If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …
Comment: ANOVA like approach of edgeR
by
SamGG
▴
350
Simply remove the cell type from the model.
design <- model.matrix(~targets$Status)
Answer: ANOVA like approach of edgeR
by
Yunshun Chen
▴
870
You could try the followings:
> design <- model.matrix(~ 0 + group)
> contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…
Answer: Identical samples after deseq2 batch effect removal
by
maripane
•
0
Thanks Michael, so is there a way to work around this issue?
Can I somehow make sure I can remove this batch effects without overcorrecti…
Votes
Awards
• All
Popular Question to
Anna
▴
20
Popular Question to
Talip
▴
10
Popular Question to
alexandre.blais
▴
50
Locations
• All
Germany, 6 minutes ago
France, 13 minutes ago
United States, 13 minutes ago
Türkiye, 29 minutes ago
United Kingdom, 49 minutes ago
Germany, 6 minutes ago
France, 13 minutes ago
United States, 13 minutes ago
Türkiye, 29 minutes ago
United Kingdom, 49 minutes ago
Traffic: 778 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