Error when using ChIPQC package

Hi, I am using ChIPQC package for assessing the quality of ChIP-Seq data. However, when I was trying to constructing a ChIPQCexperiment object, there was always an error:

chipObj = ChIPQC(samples, annotation = "hg19", blacklist = NULL, chromosome = "chr1")

FA_1 G3 FA endogenous basal 1 narrow
FB_1 G3 FB endogenous basal 1 narrow
FC_1 G29 FC endogenous basal 1 narrow
Compiling annotation...
Error in names(samplelist) <- unique(c(rownames(meta), names(controlist))) : 
  'names' attribute [6] must be the same length as the vector [5]

Did anyone know how to deal with it? Thank you.

chip-seq qc r

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updated 6.3 years ago by m.sadman.sakib

• written 7.3 years ago by owen •

You seem to have either more samples than sample names or vice versa. What is the output of length(samples) and unique(c(rownames(meta), names(controlist)))

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written 7.3 years ago by ATpoint

1 answer

I also spent almost 2 whole days trying to figure out this problem. After remapping the bams, the problem went away! In my case, I got the bam files from one of my colleagues, which was made quite some time ago. I thought, it was fine! But, I learned my lesson! Never trust bam files coming from another person!

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written 6.3 years ago by m.sadman.sakib