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HectorRDB / condiments

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
https://hectorrdb.github.io/condiments/
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fitGAM issue #8

Closed kunUCSD closed 2 years ago

kunUCSD commented 2 years ago

Hello, Thanks for building this fantastic program! I'm running it and met an issue with regard to fitGAM, as shown below. Is it because that the function does not support multi-K calculation? Thanks, Kun

conGC2 <- fitGAM(counts = conGC2,conditions = factor(conGC2$Genotype), nknots = 6, verbose = TRUE, parallel = TRUE, BPPARAM = BPPARAM) Fitting lineages with multiple conditions. This method has been tested on a couple of datasets, but is still in an experimental phase. | | 0%Error in summary.connection(connection) : invalid connection

HectorRDB commented 2 years ago

Hi @kunUCSD Thanks for your feedback. We have had many reports of the parallelization failing, which is hard to diagnose. Could you try to re-run the function without parallelization? Thanks

kunUCSD commented 2 years ago

Hi @HectorRDB Sorry for the delayed response. It works when remove parallelization. I have one more question: after identifying the differential express genes, is there a way to export the gene list with q-value and fold-change? Thanks! Best, K

HectorRDB commented 2 years ago

I'm unsure what you mean by that. After running fitGam, you can run any of the differential test that tradeSeq offer, including patternTest and conditionTest, which all returns data.frame. You can then select the columns you want and save them to a file.

On Fri, Oct 15, 2021 at 2:08 AM KunUCSD @.***> wrote:

Hi @HectorRDB https://github.com/HectorRDB Sorry for the delayed response. It works when remove parallelization. I have one more question: after identifying the differential express genes, is there a way to export the gene list with q-value and fold-change? Thanks! Best, K

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kunUCSD commented 2 years ago

Gotta it. Thanks Hector.