Question: ChIPQC for a single sample (disabling facets)
2
gravatar for Coby Viner
3.4 years ago by
Coby Viner50
University of Toronto, Canada
Coby Viner50 wrote:

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 • 894 views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Coby Viner50
Answer: ChIPQC for a single sample (disabling facets)
1
gravatar for Thomas Carroll
3.4 years ago by
United States/New York/The Rockefeller University
Thomas Carroll400 wrote:
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 COMMENTlink written 3.4 years ago by Thomas Carroll400

Thanks, Tom! I will try that for now.

ADD REPLYlink written 3.4 years ago by Coby Viner50

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 REPLYlink written 3.2 years ago by Coby Viner50

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 REPLYlink written 3.2 years ago by Thomas Carroll400

Great! Thanks, Tom!

ADD REPLYlink written 3.2 years ago by Coby Viner50

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 REPLYlink written 3.2 years ago by Thomas Carroll400

Thank you! 

ADD REPLYlink written 3.2 years ago by Coby Viner50
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