Is it somehow possible to do a chipseq experiment with two factors (treatment, no treatment), (antibody of interest, control Ig antibody)? I believe that one could do this with edgeR utilizing count data from chipseq and creating a DGEList with the group representing each individual chipseq run, and then creating a design matrix to calculate norm factors, estimate dispersion, and perform glmQLFte…
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I have performed ChIP-seq for multiple transcription factors on samples from multiple patients. All ChIPs for each patient where sequenced on different sequencing runs (i.e. TF1, TF2, TF3 for patient 1 was on one flowcell and TF1, TF2, TF3 for patient 2 was on a separate flowcell etc). I am looking at how each transcription factor's binding affinity is changing in disease vs. normal. As suc…
updated 6.2 years ago • Mthabisi Moyo
Hi,
I am using the Diffbind package to do the differential binding analysis for my ATAC-seq library. I followed the instruction to use blocking
updated 7.0 years ago • ew152
on with this command. The R version I'm using is 3.4.0 (2017-04-21), whereas the version of DiffBind is 2.4.8 .
Thanks!
Silvia
updated 6.9 years ago • Silvia
Hi,
I have generated two sets (two tissues) of histone modification CUT&RUN data, each consists of three replicates of WT and three replicates of a mutant.
I successfully made a heatmap using dba.plotProfile and now understand a bit of profileplyr to change some aesthetics.
What I couldn't understand were some details.
1. In one tissue (data set 1), the plot shows WT first on …
updated 24 months ago • Junsik
Performing `dba.count()` seems to mess up `options('mc.cores')` in the global environment
```r
options('mc.cores' = 6L)
peaks <- dba(sampleSheet = samples_df)
peaks <- dba.count(peaks)
class(peaks)
# [1] "DBA"
options('mc.cores')
# $mc.cores
# $mc.cores$mc.cores
# $mc.cores$mc.cores$mc.cores
# [1] 6
```
This then leads to downstream issues with `dba.blacklist()` and I end u…
updated 2.1 years ago • Stevie Pederson
Hi all,
I got around 100k differential peaks which someone advices me there is something wrong in my ATAC-seq analyses, so I am trying to trace back. Is this sample sheet correct? Thank you so much.![enter image description here][1]
[1]: /media/images/b797f711-4fea-46ec-967c-784dcc55
updated 17 months ago • Chris
Hi all, I used a different reference genome to align instead of GRCh38 and got this error:
result <- dba.blacklist(result)
Genome detected: Hsapiens.1000genomes.hs37d5
Applying blacklist...
No blacklist found for BSgenome.Hsapiens.1000genomes.hs37d5
No control reads specified, unable to generate greylist.
No intervals removed.
result <- dba.blacklist(result, blacklist = BSgeno…
updated 17 months ago • Chris
Hi all, I looked at the GenomicAlignments package but don't know how. Would you have a suggestion? Thank you so much! I don't know why bioconductor automatically switch to follow by message even thought I chose by email.
updated 20 months ago • Chris
Enter the body of text here
Hi
Can anyone help with the following error message. Thanks.
```r
> dbObj <- dba.count(dbObj)
Computing summits...
Error: Error processing one or more read files. Check warnings().
In addition: There were 50 or more warnings (use warnings() to see the first 50)
> dbObj$class[10:11,]
XX_ChipH3Ia_DA_Rep1
bamRead "/XX_ChipH3Ia_DA_Rep1.bam"
b…
Dear all
I am analyzing ChIPseq data.
Following code was used:
> samples <- read.csv2("sample4.csv")
> DBdata1 <- dba(sampleSheet=samples)
P359 SF Hotair 1 bed
cP359 SF Unstim 1 bed
P361 SF Hotair 1 bed
cP361 SF Unstim 1 bed
P395 SF Hotair 1 bed
cP395 SF Unstim 1 bed
> DBdata1
6 Samples, 5111 sites in matrix (7058…
updated 5.5 years ago • rapmic
Hello,
Actually I am also getting same error after printing values:
Error in if (res >= minval) { : missing value where TRUE/FALSE needed
Can you Please tell me what is going wrong?
Thanks a lot
ankit
updated 11.1 years ago • Ram
I use the following codes to model batch effect for differential analysis from different batches.
ta <- dba(sampleSheet = "diff.csv") ta <- dba.count(ta, summits=75) ta <- dba.contrast(ta, categories=DBA_CONDITION, minMembers = 2, block=DBA_REPLICATE) ta <- dba.analyze(ta) ta.DB <- dba.report(ta, contrast=1, method=DBA_DESEQ2_BLOCK, bCounts=TR…
updated 7.5 years ago • niu.shengyong
Hi I am getting the following error:
dba.plotVolcano(CR_count,th=0.1,fold=1,method = DBA_DESEQ2_BLOCK, bFlip = TRUE)
Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
This happens only when I take a .csv sample file and make a secondary file with half of the conditions present in the original, however def enough to do comparisons with. Wondering if this is …
updated 5.1 years ago • rbronste
nbsp; 'nnodes' must be >= 1__
When I use the same "examplefile.csv" file for DiffBind analysis, it works very well.
So, I don't know why the ChIPQC doesn't work.
Any help would be appreciated
updated 9.3 years ago • wangzhe335
I followd the Diffbind pipeline for a ChipSeq data:
peaksets2 = dba(sampleSheet="SampleSheet.csv",config = data.frame(RunParallel=TRUE...I followd the Diffbind pipeline for a ChipSeq data:
peaksets2 = dba(sampleSheet="SampleSheet.csv",config = data.frame(RunParallel=TRUE, AnalysisMethod
updated 5.8 years ago • hamaor
Hi,
I would like to color (1) the column bar of the antibody factor using "orange", "orchid1", and "mediumpurple1", (2) the column bar of the sex factor using "magenta", and "cyan". The commands I used and the figure I produced are below. Could you teach me how to perform it correctly? In addition, may I change the text size? Many thanks.
Best,
Gary
> histone <- dba(sampleShee…
updated 6.1 years ago • Gary
Hi wondering why with identical settings other than EdgeR vs DeSeq2 would I get 5 orders of magnitude more diff peaks with EdgeR? Thanks.
updated 7.9 years ago • rbronste
Wondering how I can go about outputting the following command which would have the chromosome map already applied? So for instance instead of "chromosome \# 26" representing the X, it is already changed in the binding matrix following counting, or is this only possible in post-processing (e.g. editing the csv output)? Thanks!
ChIP_count$binding
updated 7.0 years ago • rbronste
Hello,
I'm carrying on part of a ChIP-Seq differential analysis for the first time.
I have 6 replicates and 3 conditions; in each condition the first 3 replicates have been run separately from the other 3.
I have a couple of questions:
1) In the analysis, the consensus profile is calculated like so:
peakset <- dba(sampleSheet="/homes/fgastaldello/sumodiff/sampleSheet.csv") peakset &l…
Hi All,
I would like to find differential binding between H3K27 C vs K and H3K4 C vs K
19R_H3K27 20L_H3K27 20R_H3K27 (C)
16N_H3K27 18L_H3K27 18R_H3K27 (K)
19N_H3K4 19R_H3K4 20L_H3K4 (C)
16N_H3K4 18L_H3K4 18R_H3K4 (K)
```r
dbObj_count_summits_false <- dba.normalize(dbObj_count_summits_false,normalize="TMM",method=DBA_EDGER)
dbObj_count_summits_false$contrasts=NULL
group1_indices &…
updated 6 months ago • Dinesh
Hi, I am struggling to understand how to add a blacklist to my dba object.
I am running the standard workflow and obtaining the message below.
Despite my attempt to set `blacklist` to either a custom GRange (`blacklist`), or a constant (like `DBA_BLACKLIST_GRCH37`), I still get the same message: No blacklist found for the genome. Can I install a blacklist for this genome? Or how do I force the a…
when i put import 12 bed files in one samplesheet, i get 42967 sites in matrix.
however, when i remove one of the bed files, the number of sites in matrix changes.
the 11 and 12 bed files contain similar peak locations, as some should overlap each other...so I'm not sure if this is a problem because the files contain similar peak locations?
any ideas are appreciated! TIA
```NewSampleSheet_DBA
…
I am trying to create a dba object but get this error message:
Error in `[.data.frame`(peaks, , 2) : undefined columns selected
This is what my sampleSheet that I made from scratch looks like
![dba raw SampleSheet][1]
```
CMPdba <- dba(minOverlap=2,sampleSheet="CMP_overlapping_enhancerszeros.csv",
config=data.frame(AnalysisMethod=DBA_DESEQ2,th= 0.05,
DataTy…
updated 3.0 years ago • opheevallee
I want to run an analysis with minOverlap=1 (all peaks to be included in the consensus peakset). However, dba.blacklist changes the consensus peakset to be based on minOverlap=2. How to run dba.blacklist without changing minOverlap?
```r
dbObj_blacklist <- dba.blacklist(dbObj_initial, blacklist = blacklist_granges, greylist = FALSE)
dbObj_initial$minOverlap
dbObj_blacklist$minOverlap
sessio…
updated 12 months ago • Sam
I'm comparing knockdown ChIP (3 replicates in the green) versus control ChIP (3 replicates in the orange), but the Fold (in the grey) is much lower than I expected it to be. I know the Fold isn't just Log2FC. Could the low Fold value be caused by shrinkage adjustments due to inconsistencies between the replicates? ![enter image description here][1]
[1]: /media/images/4818964b-a81c-497e-8cbb-b7…
updated 22 months ago • slrpatty
Hi
I have a group of samples for which I'd like to ascertain if
differential binding is detectable based on a "condition" binary
variable (stored in DBA_CONDITION).
However, these samples have been processed in 4 batches (each batch
has
at least 3 samples). I would like to run a multifactorial analysis to
regress the batch effect first, and then possibly analyse any
remaining
variance across t…
updated 10.4 years ago • Giuseppe Gallone
Hi,
I wound like to get 2,913 consensus peaks that in Early stage, but not in Late stage samples (fig1). They are overlapping between T8E\_HMC & T9E\_HMC samples, but not in T8L\_HMC and T9L\_HMC samples (fig1). I have tried the dba.peakset command, but doesn't work. Could you show me how to do it correctly? The best way is to get a .bed file for the downstream analysis. Below are commands I…
updated 8.8 years ago • Gary
Hello Rory,
I am experiencing trouble trying to perform a dba with blocking factor (replicate in my case). My current dba object looks like this, and to my eyes, it has the correct format, indicating the Replicate metadata in the corresponding column
> Escape_all
ID Condition Treatment Replicate Caller Intervals FRiP
1 Ctrl_D8_1 Ctrl 0d 1 counts 12…
updated 5.3 years ago • rm1238
Hello all,
I am performing a differential accessibility analysis of ATACseq data with diffbind after using MACS2 for peak calling. However, somehow (I don't know where it goes wrong) the chromosomes are just numbered
Trying to get consensus and differential set from the same dba.count and not sure the best way to parse the two. Here is my command string:
BN<- dba(sampleSheet = "Adult_AT_BN.csv", config=data.frame(AnalysisMethod="DBA_DESEQ2",th=.05),peakFormat="narrow") BN_count<- dba.count(BN, score=DBA_SCORE_READS, fragmentSize=0) masks<-BN_count$masks M_BN_Veh<-masks$MALE & masks…
I have a question about the dba.report() output when setting bCounts=TRUE. What are the values blow each samples mean?
updated 7.4 years ago • jian.xing
Hi All,
I am trying to call differential peaks in pairs, each of my mutants (3 in total) from the same WT, within one single run.
I firstly created a dba object of my 4 strains in triplicates:
> samples
12 Samples, 419 sites in matrix (553 total):
ID Tissue Factor Condition Replicate Caller Intervals
1 …
updated 8.7 years ago • yiweihe
confused by
the dizzying array of available packages. Finally, after trying a few
tutorials (i.e. DiffBind) it became clear to me that I will need to
use parallel or cloud computing, but I am not familiar with using any
of these
updated 11.5 years ago • Christopher Howerton
Hello -
I have run a dba analysis on 4 cell types, each with 2 replicates. The way I've setup the call to dba.analyze
results in 10 contrasts. I have two questions about retrieving the results:
1) Is it possible to retrieve the DB peaks from an individual contrast, with the score column reported for all samples, in RPKM?
The code I've used is pasted below. It retrieves peaks…
updated 8.7 years ago • JD
Hi,
I would like to find differential binding between tissue ct1 condition 1 and tissue ct1 condition 2. How might I set this up in the contrast statement? Thank you!
My sample sheet looks something like this:
ID Tissue Condition Replicate
1 ct1 1 1 counts
2 ct1 &nbs…
updated 6.6 years ago • estoyanova
Hello (again),
I read lots of questions on this, but can't get it to work on my own dataset. I have histone ChIP seq data for:
1) Four different tissues
2) Two treatments
I have now a normalized count of consensus peaks which I obtained as following:
```r
#create K4 db
K4samples <- read.csv('K4samplesheet.csv')
K4 <- dba(sampleSheet=K4samples)
#count coverage for the consensus peaks
K4_c…
updated 2.7 years ago • rita.rebollo
Noticed a discrepancy in config file parameter names.
In all documentation, the DBA$config$edgeR$bTagwise and DBA$config$DESeq2$fitType parameters are structured as written here. However, in the actual DBA object they are stored as DBA$config$edgeR.bTagwise and DBA$config$DESeq2.fitType
This causes problems when trying to run an analysis on a DBA object resulting in the following error:
…
Hello,
I am have ChIPseq data from histone marks from 2 different condition (mock and treated with 2 biological replicas each) and the aim of my analysis is to study whether a particular histone mark is enriched in one condition versus the other.
I am new to bioinformatic and I don't have any statistical training and I am trying to teach myself how to normalise the data and perform the diff…
updated 20 months ago • Giulia
Hello,
I am have ChIPseq data from histone marks from 2 different condition (mock and treated with 2 biological replicas each) and the aim of my analysis is to study whether a particular histone mark is enriched in one condition versus the other.
I am new to bioinformatic and I don't have any statistical training and I am trying to teach myself how to normalise the data and perform the diff…
updated 20 months ago • Giulia
Hi Rory and Gord,
A student report a potential bug in DiffBind3. At DBA.R line 967-968,
```{r}
pv.DBA(DBA, method,bTagwise=bTagwise,
minMembers=3, bParallel=bParallel)
```
will it be better to be replaced by
```{r}
pv.DBA(DBA, method,bTagwise=bTagwise,
minMembers=minMembers, bParallel=bParallel) # minMembers = parameter from pv.contrast
```
or keep minMembe…
updated 3.5 years ago • Ou, Jianhong
Dear Antonio
I think that this problem was resolved in previous messagges, have a
look to:
https://stat.ethz.ch/pipermail/bioconductor/2012-August/047351.html?
For the complete code you could browse August mailing list.
SampleID should be unique for each sample, and moreover also bam file
file should be unique, you should make a copy of all your bamReads and
bamControl
In my example, I compar…
updated 12.2 years ago • Paolo Kunderfranco
I am using ChIPseeker to annotate my differential peaks but getting an error:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits"’
I don't have any clue to solve this error. Any suggestion is highly appreciated.
Following are my commands :
dba.show(DBdata_count_contrast_DESeq2)
…
updated 5.2 years ago • researcher
I generated a DBA object with multiple distinct contrasts, all with differentially accessible peaks. I want to generate a data frame with all these peaks and fold changes to plot a fold change x fold change plot for 2 of the contrasts.
dat <- dba.contrast(dat, group1=dat$masks$CON.treated, group2=dat$masks$CON.saline, name1="CON.TRT", name2="CON.SAL")
dat <- dba.contrast(dat, gr…
Hi,
I changed to R version 3.2.0 and DiffBind version 1.14.3. The problems are:
- The heatmap produced by
data = dba(sampleSheet="HistoneData\_C.csv", minOverlap...Hi,
I changed to R version 3.2.0 and DiffBind version 1.14.3. The problems are:
- The heatmap produced by
data = dba(sampleSheet="HistoneData\_C.csv", minOverlap=2)
plot(data)
is different that in previous version that I had …
updated 9.5 years ago • pkra
Hello All,
I have differential binding sites boject obtain from diffBind (dba.report). I am using the ChIP Seeker package to annotate the peaks but keep getting the following error:
Error...Hello All,
I have differential binding sites boject obtain from diffBind (dba.report). I am using the ChIP Seeker package to annotate the peaks but keep getting the following error:
Error in
updated 3.8 years ago • Mar Mar
When I was using DiffBind, I got the error message below from dba.plotBox():
Error in wilcox.test.default(toplot\[\[i\]\], toplot\[\[j\]\], paired
updated 7.2 years ago • xie186
Is there a way to differentiate between gain peaks and new peaks?
I want to be able to get a set of peaks that exist in two sample groups, but higher in one of them
and a set of peaks that only appear in one sample but not in the other (new peaks)
Thank you very much
Hi,
Thank you for all support so far.
I was looking back at previous posts, but couldn't find any question , so I will ask:
Is it possible to change metadata associated with dba object after dba.counts call. I am trying to understand my principal components better, and for that I would need more associated data. I could not find a way how to add extra data, so I wonde…
updated 6.5 years ago • Lauma R
Hi,
I have ChIP peaksets for three different factors in two different treatment groups. For each I have several replicates.
I have generated a consensus peak set using:
consensus<-dba.peakset(dba, consensus=c(DBA_FACTOR,DBA_CONDITION,DBA_TREATMENT), minOverlap=0.99)
Now I would like to plot the overlap between the consensus for FACTOR1 and TREATMENT1 and the individual replicate o…
updated 5.2 years ago • neumann.sylvia
MetaData <- list('ExpData' = ExperimentData)
MMD <- DBAmmd(MetaData
library('DiffBind')
DBA <- dba(sampleSheet='mmdiff2.csv', minOverlap=3
Peaks <- dba.peakset(DBA, bRetrieve = TRUE)
MMD <- setRegions(MMD
updated 5.7 years ago • Thomas Eder
Hello folks,
I tried to use plotVenn() from the DiffBind-package to compare the differential bound sites generated by DESeq, DESeq2 and edgeR. It seems to work - kinda - but...Hello folks,
I tried to use plotVenn() from the DiffBind-package to compare the differential bound sites generated by DESeq, DESeq2 and edgeR. It seems to work - kinda - but anyhow
updated 9.2 years ago • N. F.
only recently come across ChIPQC, but I find it incredibly useful, especially in combination with Diffbind. Unfortunately, I can only use some its functionalities at the moment, as I keep encountering an error when I run the
updated 7.7 years ago • Roger
__(1)__ If I have two chip samples and two input samples, and their fragmentsize are chip\_1,chip\_2,input\_1,input\_1,respectively, should I set the parameter “fragmentSize” as config = data.frame(fragmentSize = c(chip\_1 , chip\_2 , input\_1 , input\_2)) or config = data.frame(fragmentSize = c(chip\_1 , input\_1 , chip\_2 , input\_2) ? The fragmentsize varies among the four sa…
updated 7.3 years ago • xieyongjun93
Hi, I was reading [this question](https://support.bioconductor.org/p/72385/) and found I have a similar problem to the op, Igor. I'm also trying to figure out the effects of normalization on my data. Initially, I suspect that we would have a global change in our treatment vs control so based on the logic described throughout the literature bFullLibrarySize=TRUE seems appropriate; …
Hello,
Recently I have been asked to run DiffBind with an increased minimum overlap between input regions. I have tested the different between using config$mergeOverlap
updated 7 months ago • Ian D.
I am trying to analyze the differential peaks in my ATAC-seq data. I have ATAC-seq analysis on 2 biological conditions with 3 replicates in each condition. Below is my sample info:
```
ID Factor Condition Replicate Intervals
1 ATACctrl1 ctrl1 ctrl 1 8654
2 ATACctrl2 ctrl2 ctrl 2 6750
3 ATACctrl3 ctrl3 ctrl 3 5962
4 ATACe…
My testing is telling me that for union region generation 1 is the default (a gap), not -1 (1bp overlap). Negative numbers are decreasing as expected, but I am unsure about what the 1bp gap as a default represents. Does a default of mergeOverlap = 1 mean that regions will be merged if they overlap or are up to 1bp away from each other?
Thank you,
Ian
This is the default where config$merge…
updated 3 months ago • Ian D.
Hi, I am trying to look at differential binding of a number of chromatin regulatory proteins via CutandRun only at a **predefined** set of peaks (Approx. 5000 peaks).
When I carry out the analysis for different proteins at the same predefined peaks I get a different number of consensus peaks which is always less than 5000. I assumed the analysis would be carried out with the entire predefined…
updated 2.2 years ago • doherta6
I got the following error while trying to create the initiall dba object:
```r
> tamoxifen <- dba.count(tamoxifen)
Computing summits...
Error: Some read files could not be accessed. See warnings for details.
In addition: There were 12 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_20…
updated 16 months ago • Theo
Recent ...
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Comment: Merge Replicates vs Mixed Model
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Thanks, @gabrielhoffman
My understanding is that both options would still be mixed models:
Even with technical replicates (3 wells per d…
Comment: Differential Expression Genes as Independent Variables
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Dario Strbenac
★
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Also, the reason why gene abundance is the dependent variable and is iterated over is that there are far more genes than there are samples …
Comment: rrvgo::calculateSimMatrix() error
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Phila
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Thanks for sharing the solution. It helps me.
[nced cloud][1]
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Comment: Merge Replicates vs Mixed Model
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gabriel.hoffman
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170
For your proteomics data, your normalization is correct. I had assumed it was RNA-seq because that is what I think about most. When using…
Comment: What type of counts data to import for performing Isoform analysis in edgeR
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mohammedtoufiq91
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@gordonsmyth I will re-run Salmon with the --numGibbsSamples=50 option. Thank you.
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