Question

CHIP Seq Analysis by DiffBind Package

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shrinka.genetics • 0

@d85f6de8

Last seen 3.9 years ago

Hi I am using diffbind package to analyze my Chip seq data. I have bed files in my hand. I have arranged my input sample sheet (PFA). I am getting this error. Could you please help me to solve this issue?

library(DiffBind)

Data <- dba(sampleSheet="SampleInfonew.txt")

1 NA raw

Error in if (is.na(peaks)) { : argument is of length zero

Regards

Shrinka Sen

Post Doctoral Fellow

BC Cancer Research

Vancouver, Canada

SampleInfonew.txt file looks like

Sample ID Tissue Factor Condition Treatment Replicate Peaks PeakCaller CEMT_178.H3K27ac-J Breast H3K27ac Normal LP 1 CEMT_178.H3K27ac-J.bed bed CEMT_182.H3K27ac-B Breast H3K27ac Normal LP 1 CEMT_182.H3K27ac-B.bed bed CEMT_186.H3K27ac-S Breast H3K27ac Normal LP 1 CEMT_186.H3K27ac-S.bed bed CEMT_191.H3K27ac-N Breast H3K27ac Normal LP 1 CEMT_191.H3K27ac-N.bed bed CEMT_179.H3K27ac-K Breast H3K27ac Normal LC 1 CEMT_179.H3K27ac-K.bed bed CEMT_187.H3K27ac-E Breast H3K27ac Normal LC 1 CEMT_187.H3K27ac-E.bed bed CEMT_183.H3K27ac-C Breast H3K27ac Normal LC 1 CEMT_183.H3K27ac-C.bed bed CEMT_192.H3K27ac-P Breast H3K27ac Normal LC 1 CEMT_192.H3K27ac-P.bed bed

DiffBind ChIPchip • 1.0k views

ADD COMMENT • link updated 3.9 years ago by Rory Stark ★ 5.2k • written 4.0 years ago by shrinka.genetics • 0

score 0 · Answer 1 · 2020-11-27

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Rory Stark ★ 5.2k

@rory-stark-5741

Last seen 5 weeks ago

Cambridge, UK

It looks like the first column of the sample sheet is labelled Sample ID, with a space; it should be SampleID. This is throwing off the rest of the columns.

I notice there are no alignments with which to do read counting -- that is OK if all you want to do is look at overlaps (ie Venn Diagrams), but you won't be able to run dba.count() or anything else requiring reads.

ADD COMMENT • link 4.0 years ago Rory Stark ★ 5.2k

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Hi Thanks for your reply. I removed the space and it is now SampleID not Sample ID, but this error is coming. Any comments?

Data <- dba(sampleSheet="SampleInfonew.txt") CEMT_178.H3K27ac-J Breast H3K27ac Normal LP 1 CEMT_178.H3K27ac-J.bed bed NA raw Error in if (is.na(peaks)) { : argument is of length zero

ADD REPLY • link 4.0 years ago shrinka.genetics • 0

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I believe your samplesheet is tab-delimited rather than comma-separated (csv). You can either read it into a spreadsheet program and save it as comma separated, or else read it into R and supply the result to dba():

samples <- read.table("SampleInfonew.txt", header = TRUE)
Data <- dba(sampleSheet=samples)

ADD REPLY • link 4.0 years ago Rory Stark ★ 5.2k

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Hello Thanks for your reply. I changed my file format and now it ran. It gave one plot also. All file s are in same directory. Now what does the error means?

samples <- read.table("SampleInfomod.txt", header = TRUE) Data <- dba(sampleSheet=samples) plot(Data) Datamod <- dba.count(Data, summits=250)

Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score, : Can't count: some peaksets are not associated with a .bam file.

ADD REPLY • link 3.9 years ago shrinka.genetics • 0

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In my very first response, I noticed that you had not included any bam files (which contain the aligned sequencing reads) in your sample sheet. These must be included for each sample in order to generate a count matrix.

ADD REPLY • link 3.9 years ago Rory Stark ★ 5.2k