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hbc / bcbioRNASeq

R package for bcbio RNA-seq analysis.
https://bioinformatics.sph.harvard.edu/bcbioRNASeq
GNU Affero General Public License v3.0
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DESeq2 plot functions not found with bcbioRNASeq #184

Closed VictoriaPatten closed 2 years ago

VictoriaPatten commented 2 years ago

Hi, I am using bcbioRNASeq and working from the linked workflow paper: Steinbaugh MJ, Pantano L, Kirchner RD, Barrera V, Chapman BA, Piper ME, Mistry M, Khetani RS, Rutherford KD, Hoffman O, Hutchinson JN, Ho Sui SJ. (2018).

I have gone through all of the QC steps and created the plots no problem, but now when I move on to the Differential Expression Analysis using DESeq2 I keep running into trouble. I keep getting errors like Error in plotMeanAverage(res) : could not find function "plotMeanAverage" and the same happens for the plotVolcano(res). The alphaSummary function was also not found.

Please can you advise on how to proceed as I can't seem to create any DGE plots.

Is there updated documentation on using bcbioRNASeq and doing DGE analysis, or is the 2018 article above the only one?

Thanks.

mjsteinbaugh commented 2 years ago

@VictoriaPatten I know how to fix the functional analysis template to get your dataset to work. I'll push a couple of changes to DESeqAnalysis and AcidGSEA that should fix the issue.

mjsteinbaugh commented 2 years ago

The minimal example won't work in the R Markdown template, it was just to check that your installation is working as expected

VictoriaPatten commented 2 years ago

Hi @mjsteinbaugh have you managed to push those changes? Sorry to bug you about it but my thesis submission deadline is next week so I'm on the wire and stressing to get this finished.

mjsteinbaugh commented 2 years ago

@VictoriaPatten Sure thing, I'll send an update later today

mjsteinbaugh commented 2 years ago

@VictoriaPatten Almost done, will push a couple of updates to AcidGSEA and bcbioRNASeq in the morning. I'll upload the R Markdown templates and the render files to your Google Drive tomorrow.

mjsteinbaugh commented 2 years ago

OK I think the AcidGSEA 0.8.5 update I just pushed should fix the issue you're having with the RankedList generator step for Ensembl-to-Entrez identifier mapping. I'll double check the Markdown template and send you an update in the morning.

mjsteinbaugh commented 2 years ago

@VictoriaPatten This should be resolved with the FA template update. Let me know if you run into any additional issues.