User: jared.andrews07

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Posts by jared.andrews07

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Multi-factor blocking in DiffBind
... I was wondering if it's possible to account for multiple factors when analyzing samples in DiffBind. I want to block for potential batch effects as well as treatment conditions, but I'm unsure how to do so (or if it's even possible). The docs make it clear how to block for one factor, but don't make ...
diffbind multiple factor design differential binding analysis written 6 weeks ago by jared.andrews070 • updated 6 weeks ago by Rory Stark2.1k
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Answer: A: Unhelpful Errors Running ChIPQC on Computing Cluster
... Yeah, I'm not sure what the issue was here. I managed to get it running locally, so I'm just going to chalk it up to issues with R on the cluster. It does not like running in parallel though, I always have to run it in serial to get it running. Thanks for checking up on it. ...
written 9 weeks ago by jared.andrews070
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Comment: C: Unhelpful Errors Running ChIPQC on Computing Cluster
... Excellent, thank you. `ChIPQCsample` works just fine on my individual samples, so I don't think there's anything wrong with any of my bam or peak files. I may just go ahead and create the sample objects for each of my samples and try running it with a list of those, inconvenient as it is. Also, it t ...
written 3 months ago by jared.andrews070
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Unhelpful Errors Running ChIPQC on Computing Cluster
... I'm having issues running ChIPQC on a computing cluster, and the errors being thrown aren't particularly helpful. The code: library(ChIPQC) my_experiment = ChIPQC(experiment="CellLine_Experiment_Sheet.csv", annotation="hg19") ChIPQCreport(my_experiment, facetBy=c("Tissue", "Treatment")) warnings ...
chipqc chipqcreport written 3 months ago by jared.andrews070

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