Question

ChIPQC for a single sample (disabling facets)

2

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Coby Viner ▴ 50

@coby-viner-10939

Last seen 3.5 years ago

University of Toronto, Canada

Using the same commands, and session information as C: ChIPQC without peak calls, I encounter the below error upon attempting to run: ChIPQCreport(experiment, facet=F)

Saving 7 x 7 in image
Error: Faceting variables must have at least one value
Execution halted

How do I correctly disable faceting? I only have a single sample in this case, so there is nothing to facet over. Would it be possible for ChIPQC to automatically detect this case?

ChipQc chipqc • 2.7k views

ADD COMMENT • link 8.3 years ago Coby Viner ▴ 50

score 1 · Answer 1 · 2016-07-06

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Thomas Carroll ▴ 420

@thomas-carroll-7019

Last seen 24 months ago

United States/New York/The Rockefeller …

hi Coby, You have specified this correctly but this case of using ChIPQCreport with a one sample experiment is not being correctly handled. I will need to check in a new version and let you know to update the ChIPQC package for a proper fix. In the meantime, since this a one sample experiment, you could use ChIPQCreport on a ChIPQCsample object instead. Using the example data in package ># Get a list of ChIPQCsample objects from a ChIPQCexperiment > tamoxifenSampleList <- QCsample(tamoxifen) > sampleOfInterest <- tamoxifenSampleList[[1]] ># > ChIPQCreport(sampleOfInterest) I'll let you know when new release is available. best, tom On Wed, Jul 6, 2016 at 7:11 PM, Coby Viner [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Coby Viner <https: support.bioconductor.org="" u="" 10939=""/> wrote Question: > ChIPQC for a single sample (disabling facets) > <https: support.bioconductor.org="" p="" 84754=""/>: > > Using the same commands, and session information as C: ChIPQC without > peak calls <https: support.bioconductor.org="" p="" 84072="" #84153="">, I encounter > the below error upon attempting to run: ChIPQCreport(experiment, facet=F) > > > > Saving 7 x 7 in image > Error: Faceting variables must have at least one value > Execution halted > > > > How do I correctly disable faceting? I only have a single sample in this > case, so there is nothing to facet over. Would it be possible for ChIPQC to > automatically detect this case? > > > > ------------------------------ > > Post tags: ChipQc, chipqc > > You may reply via email or visit ChIPQC for a single sample (disabling facets) >

ADD COMMENT • link 8.3 years ago Thomas Carroll ▴ 420

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Thanks, Tom! I will try that for now.

ADD REPLY • link 8.3 years ago Coby Viner ▴ 50

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Hi Tom,

I was wondering if you had an update on a time-line for the next ChIPQC release?

We are currently preparing a publication, which provides a brief protocol to perform ChIP-seq quality control, using ChIPQC. It would be useful for us to be able to provide the standard commands in all instances, obviating a necessity to outline this workaround.

Thanks,

Coby

ADD REPLY • link 8.2 years ago Coby Viner ▴ 50

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hi Coby,

I'll check in over the weekend then you shouldn't need the workaround.

I made it easier to generate a report from ChIPQCsample objects as well as fix the 1 sample and facet=F problems.

I just need to fix the updated documentation and I will update you here to let you know it is available in Bioconductor release branch.

best,

tom

ADD REPLY • link 8.2 years ago Thomas Carroll ▴ 420

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Great! Thanks, Tom!

ADD REPLY • link 8.2 years ago Coby Viner ▴ 50

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hi Coby,

New release is checked in ChIPQC 1.8.5. Should be available from source now and building tonight.

Here is an example of disabling facets for the report.

data("tamoxifen_QC")
ChIPQCreport(tamoxifen,facet=F)

Let me know if you have any problems.

best,

tom

ADD REPLY • link 8.2 years ago Thomas Carroll ▴ 420

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Thank you!

ADD REPLY • link 8.2 years ago Coby Viner ▴ 50