CHIP Seq Analysis by DiffBind Package
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@d85f6de8
Last seen 3.2 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 • 824 views
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Rory Stark ★ 5.1k
@rory-stark-5741
Last seen 8 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.

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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

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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)
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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.

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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.

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