Bioconductor Forum

hi，I run the code successfully: ```r yap <- dba.count(yap) yap <- dba.contrast(yap,categories=DBA_CONDITION,minMembers=2) yap 4 Samples, 31676 sites in matrix: ID Condition Treatment Replicate Caller Intervals FRiP 1 IP1 IP IP 1 counts 31676 0.53 2 IP2 IP IP 2 counts 31676 0.56 3 IgG1 IgG IgG 1 counts…

DiffBind

updated 4.8 years ago • 浩然

Hi, When I run dba.counts, it showed an error below (fig1): Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score, : Some read files could not be accessed. See warnings for details. In addition: Warning message: not accessible Is it because that I don’t have bamControl for 6 ATAC-Seq samples (fig2)? How can I overcome this issue? Thank you so much. Best, …

DiffBind

updated 9.5 years ago • Gary

do I need to create something else? Right now this is my R script: ``` library(ChIPQC) library(DiffBind) library(tidyverse) sampleSheet <- read.csv("meta/peaks.xls") db <- dba(sampleSheet =sampleSheet) ``` When I look at the

ChipSeq ChIPSeqData chipseqDB

updated 3.2 years ago • stacy.genovese

and your samples may not be representative; and 2) because the statistical techniques that DiffBind relies on (embodied in the edgeR, DESeq, and DESeq2 packages) require replication to properly calculate confidence...statistics. Technically, DiffBind will handle this comparison. You may want to do some simpler overlaps (dba.plotVenn, dba.overlap) to detect regions...Roy" <roy.blum at="" nyumc…

DiffBind DESeq2 DiffBind DESeq2

updated 12.0 years ago • Rory Stark

not exist, also good. ``` Result: Nope, no chr21 in any of the 8 peak files ## What does DiffBind see? ```r > sample = dba(sampleSheet=read.csv('sample_table.csv'), \ peakFormat='bed', scoreCol=5, bLowerScoreBetter=FALSE

DiffBind

updated 3.7 years ago • Mehmet

Hello, I hope you are doing well and are safe. I wanted to reach out since I have been having issues with loading my broadPeaks and/or the .xls outputs from MACS2 into DiffBind. Would appreciate any help you can provide, thank you! My thinking is there might be something wrong with the way I am...since I have been having issues with loading my broadPeaks and/or the .xls outputs from MACS2 into Di…

DiffBind

updated 2.7 years ago • Mark

I have done chip-seq and called differential binding peaks between WT and mutant conditions using "diffbind" package. I annotated the two lists of condition specific peaks to nearest genes and found that 537 genes were annotated

annotation

updated 6.3 years ago • vanhzh

New to R, but enthusiastic to start easing into the world of bioinformatics analysis. Currently partway through my PhD, creating and testing new protocols (ChIP-Seq, bioinformatics analyses) solo in a small research group without an expert or experienced Post-Doc/PI to provide guidance. I've read through the DiffBind Vignette a few dozen times, and followed through a video tutorial hosted on t…

DiffBind

updated 3.6 years ago • niimabear

a better way to look at a differential binding site for specific regions? (I'm using R v3.3.1 and DiffBind v2.2.12) Many thanks, Sylvia &nbsp

dba.count dba chipseq diffbind

updated 8.1 years ago • sylvia

Hi I am making a SummarizedExperiment from a DiffBind dba.peakset in the following way (to use in DESeq2): rangedCounts <- dba.peakset(Adult_count, bRetrieve=TRUE) nrows

diffbind matrix summarizedexperiment rangedCounts

updated 6.3 years ago • rbronste

I have a pair of chipseq. One is really bad. Mapping failed. I was wondering if it's possible to analyse only one without the pair ? Other question : I tried to do the analyze with both of the samples even is one is not very good. I did two different things : the first time I set the rule that peaks must be in both replicates...that gaves me 1116 differential peaks.

dba_chip_consensu…

diffbind

updated 8.4 years ago • ZheFrench

Hi, once loaded a dba object, and already computed the counts, is there a way to change only the design conditions column in order to perform the further steps? I just want to shuffle the sample conditions without computing the counts again in order to perform the contrasts. Thanks, inzirio

diffbind conditions edit

updated 6.5 years ago • inzirio

Hi, I know that those are very stupid question but is there a way to obtain an "exportable" data frame (something like a txt file) containing the raw count for each peak in each sample obtained with dba.count without performing all the differential analysis? Is there the possibility to obtained data frame containing the consensus peak set generated in my analysis? Thank you so…

diffbind

updated 10.4 years ago • barbara.mariotti

Hello Rory, I have the following experimental design, Rep1 and Rep2 are collected in different batches, with batch effect obvious from PCA plots: Sample Condition Replicate 1 A 1 2 A 2 3 B 1 4 B 2 I used the following code to account for batch effect: db.counts &…

diffbind

updated 6.2 years ago • liruiradiant

If I want to asses the overlapping between: Differential binding sites between T1 and T2 (Control samples (untreated)) independent of the mouse type

> myDBA = dba.contrast(myDBA, group1=myDBA$masks$T1, group2=myDBA$masks$T2, block=DBA_CONDITION, name1="T1", name2="T2")

And differential binding sites of T1 taking into account the mouse type
> myDBA = dba.contrast(myDBA, group1=myDBA$…

diffbind

updated 11.0 years ago • sergio.espeso-gil

Dear, I am new to differential ChIPseq analysis. One condition has 6 biological replicates and the other 3. I did not perform the experiment, I just perform the analysis. I started with loading the data:

prol.10 = dba(sampleSheet="macs10_30.csv")

This resulted in a total of 7602 peaks with 47 present in at least 2 samples. This indicates that the experiment was not very reproducible. I furth…

diffbind merging_peaks

updated 8.9 years ago • veronique.storme

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 peak callers for each factor before generating a consensus across the factors. Is there any way i can achieve this without having to create multiple DBA's? My current workflow is: - create DBA with ALL sample…

diffbind

updated 6.0 years ago • Jim

Hello, all I am just wondering if I am misunderstanding the consensus peak. I am under the impression that this is the number of peaks contained within a set. for example all peaks in control replicates. When using overlap the last number matches my venndiagram, but when added the consensus peak to my set it does not:



dba.overlap(test,test$masks$het  ,mode=DB…

diffbind

updated 9.0 years ago • cperez5

Dear Rory, I found the solution to my previous questions. However, now I am comparing the results from the available edgeR analysis with the robust edgeR pipeline with QL method based on raw read counts. This is the pipeline that I want to use. I found the raw read counts by

reads.5 = dba.count(prol.5, peaks=NULL, score=DBA_SCORE_READS)
bindingMatrix.5 = dba.peakset(reads.5, bRetrieve=TRUE, …

edger diffbind raw reads

updated 8.8 years ago • veronique.storme

I have run ATAC-seq on 4 samples (2 groups with 2 samples each) and I am wanting to differential peak calling between groups but I noticed that when I generate a report of my analysis with dba.report() two of the samples have the exact same count values across all peaks (6.61 for both c1s and c3r). the samples are grouped by condition (slow vs rapid). For this experiment c1s and c4s are in the "s…

diffbind dba.count dba.report

updated 6.3 years ago • chadnewton

Hi All, Longtime lurker hoping to get guidance on a package that may best fit my RNA-chromatin data. The technique is similar to: https://www.nature.com/articles/nbt.3968 My library generates pairs of RNA in close proximity to DNA. I have replicates for two time points and generated an interaction score for any RNA to 1KB bins of the genome. The scores are fold enrichment over background an…

Differential Peak Calling DiffBind DESeq2

updated 6.6 years ago • jkanbar

marks (2 for silencing and 1 for activation) each mark has three replicates. when I run the diffBind package I have three contrast: Silence1-Activation Silence1-Silence2 Silence2-Activation When I run dba.plotBox

chip-seq diffBind sequence_analysis

updated 5.5 years ago • Mar Mar

to the parameter maxk when calling the function locfit. But I'm not sure how to edit this number in DiffBind. Could you help me solve the problem? Thanks a lot. </pre> P.S. I also tried method=DBA\_ALL\_METHODS and got the same problem

atac-seq diffbind

updated 8.8 years ago • zhaolin20042008

div class="preformatted">Hi, I am trying to use DiffBind to analyze my ChIP-Seq data. I used MACS2 as my peak caller and to adjust for input. I am able to use dba to load in the data...any help to troubleshoot. Thanks in advance, Ravi Code, traceback, and sessionInfo: > library (DiffBind) > > samples = read.csv ("~/Desktop/Data/Acetyl_sampleSheet.csv", header = T) Wa…

DiffBind DiffBind

updated 11.6 years ago • Ravi Karra

Hi, I'm working with diffbind R package to perform differential analysis on h3k27ac peak data, however, in my case I have to generate a new DBA object...containing custom read count across a number of patient samples. Following diffbind instructions, I tried to generate the DBA object starting from the 'dba' command using a Datasheet with all the required...CD34_control_PE" "CD34_control_PE" …

DiffBind dbaobject

updated 3.1 years ago • francesco.gandolfi

MACS2 using 2 reps to produce a set of peaks in a highly consistent manner, I upload the data with DiffBind (dba function), creating a consensus peak set of 127,994. Since our dataset is so large, in order to minimize the number

DiffBind Consensus peak

updated 5.9 years ago • rmendez

peaks obtained from pooled-ChIP analysis, with different ChIP.bam and the same Pooled-input.bam for DiffBind analysis. SampleID,Tissue,Factor,Treatment,Condition,Replicate,Peaks,bamReads,bamControl IP-6C,WT,TF1,Fullmedia

diffbind

updated 11.0 years ago • eva.pinatel

lt;- "a" > peak@metadata $test [1] "a" ``` But I also noticed some package I always used, like [DiffBind](https://bioconductor.org/packages/release/bioc/html/DiffBind.html), [ChIPseeker](https://bioconductor.org/packages

GenomicRanges

updated 4.7 years ago • shangguandong1996

Dear Rory, Thank you for your efforts in DiffBind. A basic overview of my dataset. There are two conditions, each having two bio-replicates. I'd like to run differential...be so grateful if you have any ideas. Many thanks in advance! My code is as follows. ```r library(DiffBind) samples <- read.csv("in.info.csv") tamoxifen <- dba(sampleSheet=samples) library(rtracklayer) mype…

DiffBind diffbind

updated 2.7 years ago • littlefishes20

Hello, I run diffbind to find DB between my two samples( control and phosphate deficiency) with two replicates. i choose deseq2...software to find DB and I got some DB , but I could not understand why I did not get any DB from diffbind.  my samplesheet : SampleID Tissue  Factor Condition Treatment Replicate 1     WTC1  …

diffbind

updated 8.6 years ago • mforoo1

Hello, do you know how to resolve the following error? Error: BiocParallel errors 1 remote errors, element index: 1 0 unevaluated and other errors first remote error: Error in DataFrame(..., check.names = FALSE): different row counts implied by arguments while executing the code: > results <- dba.analyze(contrast) > mutants <- dba.re…

BiocParallel DiffBind

updated 7 months ago • this_is_me_trying

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 containing t…

DiffBind

updated 15 months ago • Haiping

With `dba.plorProfile` function I can calculate the profiles but while plotting, I get the following error: ```r > profiles <- dba.plotProfile(dbobj, sites=overlaps) Generating profiles... > dba.plotProfile(profiles) Plotting... Error in heatmap_width_pt * raster_quality : non-numeric argument to binary operator ``` Can anyone help me with this? Thank you in advance.

DiffBind

updated 4.1 years ago • bhanu.chandra1

Hi all, Would you please suggest what wrong in this case? I pretty much run the same code as before. Thank you so much. result <- dba(sampleSheet=samples) result <- dba.blacklist(result) result <- dba.count(result, bParallel=FALSE) result <- dba.count(result) result <- dba.normalize(result) result <- dba.contrast(result, minMembers=2) result <- …

DiffBind

updated 2.5 years ago • Chris

Hi all, I have 4 samples which are 4 conditions but when I made some plots, I got only 2 conditions. ![enter image description here][1]! Does this plot mean ws has chromatin more chromatin open (gain) than wf sample? When I rerun the code, I got all 4 conditions but the plot is quite different. There are no gain and loss but only sites. Thank you so much! ![enter image description here][2] [1…

DiffBind

updated 2.6 years ago • Chris

Hi all, Would you suggest how to fix this error? I have only 2 replicates for the control and 2 replicates for the diseased group. Thank you so much. result <- dba.analyze(samples, bParallel=FALSE) [W::hts_idx_load3] The index file is older than the data file: /labs/PI/atacseq_output_03172023/bwa/merged_library/DISEASED_REP2.mLb.clN.sorted.bam.bai Normalize DESeq2 wit…

ATACSeq

updated 2.8 years ago • Chris

Hello all, Seem there is something wrong with my samples samples <- read.csv("samplesheet_DiffBind.csv") result <- dba.analyze(samples) Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator I understand what this error means but don't know what is the cause. Would you suggest to me how to fix this? Thank you so much!

DiffBind ATACSeq

updated 2.8 years ago • Chris

Enter the body of text here 1: How to extract the counts of each replicate after dba.count while doing the occupancy analysis? I would like develop a genomic ranges object that consist of consensus peaks (chr, start, end,) and in addition to score two column showing the normalized counts of each replicate in only these consensus peak set. 2: Also, why counts(48923) are different than peak…

DiffBind

updated 4.5 years ago • faiza

I have the following design matrix: ```r 8 Samples, 475298 sites in matrix: ID Factor Condition Replicate Reads FRiP 1 ep_293T_siNeg_R1 eprint siNeg 1 9951758 0.76 2 ep_293T_siNeg_R2 eprint siNeg 2 13656477 0.77 3 ep_293T_siFUS_R1 eprint siFUS 1 14988942 0.73 4 ep_293T_siFUS_R2 eprint siFUS 2 21025467 0.75 5 input…

DiffBind

updated 4.5 years ago • Alexandre

Dear, I would like to determine summit value for a list of enhancers from a public database. I use these lines: ```r # load features table: 3 columns Chr, Start, End features <- read.table("GeneCards_GeneHancer", header = T) # create exp.dba object exp.dba <- dba(sampleSheet = "ATAC_sampleSheet.csv") # count with summits = T exp.dba <- dba.count(DBA = exp.dba, peaks = featur…

DiffBind

updated 5.0 years ago • mdidish

Hi, I have a problem with dba.report, which gives the error below. This is limited to edger, while it works fine with DESeq2. Any idea of why? Ivan > # edgeR > dbind.report.edger <- dba.report(DBA = dbind_de, contrast = 1, method = DBA_EDGER, th = fdr_thr, fold = lfc_thr) Error in .Call2("C_solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : In range 1222: at…

DiffBind

updated 4.7 years ago • Ivan

Hello, Could someone please clarify what the fragmentSize option really means? From the manual under the dba function it states "numeric with mean fragment size. Reads will be extended to this length before counting overlaps." but under the dba.count function it states "This value will be used as the length of the reads. Each read will be extended from its endpoint along the appropriate strand…

DiffBind

updated 4.9 years ago • Jürgen

composition differences during normalization?** I have read the relevant sections of both the DiffBind and csaw documentation thoroughly, but both assume identical spike-in levels across all samples. Are my thoughts

csaw ChIPseq DiffBind

updated 2.2 years ago • jared.andrews07

Greylist."* To figure out what was wrong, I also moved one of my bam files to the sample folder of Diffbind vignette and changed the file name. I run dba() dba.analyze(tamoxifen) and they worked. So I am confused about what the

DiffBind

updated 5.0 years ago • ahua217

Hi, I would like to use custom colors instead of default colors in dba.plotHeatmap. The below is my command lines and error messages, could you help me to trouble shooting? Many thanks. Best, Gary > atac <- dba(sampleSheet = "atac.csv",peakFormat = "bed") CTNNB1\_G8\_13 13 CTNNB1 RCAS Treat 1 MACS2 CTNNB1\_G8\_14 14 CTNNB1 RCAS Treat 2 MACS2 CTNNB1\_G8\_15 15 CTNNB1 RCAS …

diffbind color

updated 9.1 years ago • Gary

Hi there, I’ve been using the dba.PCA function (Package _DiffBind_ version 1.14.6) in the standard way described in the documentation. So far, I have two very related questions: 1. How can I retrieve the scores, loadings, eigenvalues from dba.PCA? 2. I’m interested in understanding how dba.PCA works. To do so I’ve unsuccessfully tried to recreate the PCA myself, the r…

diffbind pca

updated 10.2 years ago • renanec

Hi I use the command below to draw a heatmap below. However, I would like to label DBA\_CONDITION with mediumpurple1 and orange; and label DBA\_TISSUE with lightskyblue and orchid1. Could you show me how to do it? Moreover, may I use Sex instead of CONDITION ,and use feather type instead of TISSUE in the figure, and how to do it? > dba.plotHeatmap(h3k27ac, attributes = DBA\_ID, ColAttributes…

diffbind

updated 8.4 years ago • Gary

Hi Rory, I wonder, if it is possible to extract counting data (after performing dba.count) from a resulting DBA object in csv format where consensus peak names are in the first column, peak positions are in the second/third/forth colums (chromosome, start, end) and normalized number of reads for each sample are in subsequent columns. Regards Konstantin

diffbind read counts extract data

updated 7.8 years ago • k.panov

Hi, I extracted my consensus peakset from the DBA object after counting. I filtered this list to remove outliers and other criteria. I would like to change the consensus peakset in my DBA object now, using my filtered list. I extracted the consensus peaks like this: countTable <- dba.peakset(sampleCounts, bRetrieve=T,DataType=DBA\_DATA\_FRAME) How do I put it back into the DBA obje…

diffbind

updated 9.4 years ago • sarah.blackstone7734

I was trying to analyze differential binding for four different set of experiments done in duplicate SampleI Tissue Factor Condition Replicate bamReads ControlID bamControl Peaks PeakCaller NS_1 NS Un NS 1 15-011-001.sorted.bam ns_s1_peaks.narrowPeak narrowPeak NS_2 NS UN NS 2 15-011-005.sorted.bam ns_s2_peaks.narrowPeak narrowPeak HSF_…

diffbind

updated 5.6 years ago • bony.dekumar

Is it possible to create a new dba object based on a subset of the samples in a previous call to dba.count, or dba.analyze? Basically, I would like analyze subsets of samples as seperate analyses, without recounting. I'm analyzing atac-seq data, which is paired end and >50 million reads per sample for 20-30 samples. I've been using the summarize overlaps method to …

diffbind

updated 10.3 years ago • ashley.doane

I am plotting all sites based on p-value and would like to do two things: 1. Remove everything that aligns as a straight line at 1. 2. Pseudocolor points on the plot that have a high adjusted p-value score a different color. Thanks.

diffbind chipseq volcanoplot ggplot2

updated 8.3 years ago • rbronste

What will be the best use of the dba.peakset and minOverlap to extract 3 datasets that have the common peaks, the peaks enriched in c-Jun ChIP and the ones enriched in JunB ChIP. my dataset looks like: CHIP_seq_Goett_peaks_ALL 4 Samples, 33031 sites in matrix: ID Tissue Factor Condition Replicate Caller Intervals FRiP 1 Cell1px8 epithelial junB Cell1_…

diffbind chip-seq dba.peakset

updated 6.3 years ago • theodore.georgomanolis

Hello, I was wondering if there was an option to run the differential analysis without the normalisation step ? Apparently there is an option like that for some plots but I can't happen to find anything for the differential analysis. Thank you for your time Thomas

diffbind differential binding analysis

updated 5.2 years ago • Thomas

Wondering what can cause skewing in an MAplot as seen below?

diffbind deseq2 maplot

updated 8.3 years ago • rbronste

I would like to save separately differential binding sites fold>0 and fold<0 reported by sum(myDBA.DB$Fold<0) sum(myDBA.DB$Fold>0) I am trying to use the fold option in db.report but it doesn't allow to add > or < . How I can do then this? Thanks a lot

diffbind

updated 11.2 years ago • sergio.espeso-gil

How to change the default scatter plot colors of dba.plotMA function? --- Senthil

diffbind

updated 8.9 years ago • Senthil

I used DiffBind to get a GRange object with differentially bound genomic sites. This GRange also contains several numeric columns...but this throws an error. I'm guessing because this references the Tx.Db GRange and not my DiffBind GRange? ``` columns = c("tx_id", "tx_name", "Conc")) ``` I'm sure there is a simple way to accomplish this, but I'm fairly inexperienced

GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind

updated 5.5 years ago • vanbelj

I am trying the following code and getting an error I am unsure how to fix: <pre> countData<-read.csv("p14_binding.csv") rownames(countData) <- countData[,1] countData[,1] <- NULL sampleNames<-c("MB1", "MB2", "MB3", "FB1", "FB2", "FB3", "MM1", "MM2", "MM3", "FM1", "FM2", "FM3") sampleSex<-c("male", "male", "male", "…

deseq2 deseq differential binding analysis

updated 8.3 years ago • rbronste

which supports the idea that the error can be attributed to the new version. Interestingly, however, DiffBind works just fine. Thanks for your time. Roger

chipqc chipqcreport

updated 8.6 years ago • Roger