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!
…
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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…
updated 3.2 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…
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…
updated 3.4 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…
updated 4.9 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 )
…
updated 6.5 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 …
updated 7.0 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…
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? 
updated 8.6 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
updated 7.7 years ago • bwassie
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\…
updated 7.0 years ago • zhaolin20042008
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…
updated 15 months 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 …
updated 3.8 years ago • ahua217
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…
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…
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…
updated 17 months 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…
updated 18 months 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
updated 6.6 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
updated 2.8 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…
updated 15 months 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
updated 13.1 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
updated 7 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
updated 8.4 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
ChIPQC\_1.8.3 DiffBind\_2.0.1 SummarizedExperiment\_1.2.3 Biobase\_2.32.0
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
updated 5.2 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…
updated 8.4 years ago • cattapre
_1.26.0 ChIPQC\_1.12.2 DiffBind\_2.4.6 SummarizedExperiment\_1.6.3 DelayedArray\_0.2.7
 
updated 7.4 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
updated 6.8 years ago • michal.inbar
attached packages:
\[1\] ChIPQC\_1.12.3 DiffBind\_2.4.8 SummarizedExperiment\_1.6.4 DelayedArray\_0.2.7
 
updated 7.2 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…
updated 7.4 years ago • tirza.doniger
Hello,
I have the following samples, with three replicates in each of them:
My biological setup:
* I started with 2 samples of Precursor (considered also as 00h): KO or WT.
* …
| 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 |
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!
updated 7.8 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/
updated 5.0 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
updated 7.8 years ago • rbronste
I have ChIP-seq datasets as the following:
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 + …
| 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 |
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…
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…
updated 9.6 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\…
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…
updated 9.1 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…
updated 5.0 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
updated 6.2 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",…
updated 7.8 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
Hi,
When I try to calculate the overlap rate between peaksets, I get the following errors:
> names(broad_gtsf1$masks) # just list all
[1] "K562" "H3K9Me3" "75" "313" "WT" "Mutant" "counts" "Consensus" "Replicate.1" "Replicate.2" "Replicate.3" "Replicate.4" "All"
[14] "None"
> dba.overlap(broad_gtsf1, …
updated 5.5 years ago • aviv.de-morgan
How can I control colors for different colAttributes: one as Factor and other is Condition. Can I use different colors for these two cola attributes? Additionally, How can I have the color annotation for each factor and condition. Kindly help.
Thanks!
updated 5.3 years ago • researcher
Hi!
When I use the function dba to create a dba object, I always encounter the error :
Error in if (file.info(peaks)$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… |
updated 6.8 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…
updated 9.3 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…
updated 6.2 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…
updated 10.6 years ago • Dan Tenenbaum
Bioconductors:
We are pleased to announce Bioconductor 2.12, consisting of 671
software packages and more than 675 up-to-date annotation packages.
There are 65 new software packages, and many updates and improvements
to existing packages; Bioconductor 2.12 is compatible with R 3.0,
and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This
release includes an updated Bioconductor
Ama…
updated 9.4 years ago • Dan Tenenbaum
Bioconductors:
We are pleased to announce Bioconductor 2.11, consisting of 610
software packages and more than 650 up-to-date annotation packages.
There are 58 new software packages, and many updates and improvements
to existing packages; Bioconductor 2.11 is compatible with R 2.15.1,
and is supported on Linux, 32- and 64-bit Windows, and Mac OS. This
release includes an updated Bioconductor Am…
updated 12.2 years ago • Dan Tenenbaum
Bioconductors:
We are pleased to announce Bioconductor 2.13, consisting of 749
software packages, 179 experiment data packages, and more than 690
up-to-date annotation packages.
There are 84 new software packages, and many updates and improvements
to existing packages; Bioconductor 2.13 is compatible with R 3.0.2,
and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This
release in…
updated 11.1 years ago • Dan Tenenbaum
Recent ...
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