Question

ChIPQC error: 'names' attribute [9] must be the same length as the vector [7]

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sonyuna90 • 0

@sonyuna90-21186

Last seen 5.5 years ago

Hi, I have errors after running ChIPQC.

ChIPQCreport(chipObj, reportName="ChIP QC report: H3.3", reportFolder="ChIPQCreport") Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Using Sample as id variables Saving 7 x 7 in image Saving 7 x 7 in image Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", : 'names' attribute [9] must be the same length as the vector [7] In addition: Warning message: Removed 300 rows containing missing values (geom_path).

I can't get the QC summary and I am not sure if I can trust even the image files after generating from this command line. Any idea and I saw the posting with similar issues, but I couldn't find any answer.

Thank you in advance.

software error • 3.0k views

ADD COMMENT • link updated 4.9 years ago by vermasrikant • 0 • written 5.5 years ago by sonyuna90 • 0

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I have the same error and just reverted my R to R-3.5.1 to solve the problem. I think the issue is with 3.6.1 that QCmetrics is getting different number of items to that of the ChIPQCreport() function.

and I think that's what shengqh did for the bug fix.

@Rory Stark, we are setting up an automated pipeline with a ChIPQCreport running inside at HSPH Bioinformatics Core. Will there be a bug fix done soon for this? Thanks.

ADD REPLY • link 5.2 years ago joonyoon.jay ▴ 20

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I am experiencing the same error and also cannot find a solution online... any insights to resolving this would be much appreciated

ADD REPLY • link 5.5 years ago wa23 • 0

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I fixed the problem in my forked one tonight, you may install it and have a try. I will contact author to fix the bug later.

https://github.com/shengqh/ChIPQC

ADD REPLY • link 5.3 years ago shengqh ▴ 10

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Hello, I still get the error. I don't know what to do.

ADD REPLY • link 4.8 years ago mudithekanayake • 0

score 0 · Answer 1 · 2020-02-17

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vermasrikant • 0

@vermasrikant-13625

Last seen 2.8 years ago

India

I got the same error with R-3.6.1 and R-3.6.2. Following @joonyoon.jay's recommendation, I tried with lower R version R-3.5.3, and it resolved the issue.

ADD COMMENT • link 4.9 years ago vermasrikant • 0

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I have the same issue. Earlier I had to update from R-3.5 to newest version because I had issues with installing Bioconductor and ChIPQC because of the older version. After updating it worked and I could come this far to get this error. If I change it to 3.5 then will package work?

ADD REPLY • link 4.8 years ago mudithekanayake • 0