DE analysis packages not detecting Splat DE simulated genes
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Last seen 14 months ago

Hi, I hope this is an appropriate question forgive me if not however I am currently doing a DE analysis benchmark study and using Splatter as my scRNA-seq data simulator. I have estimated parameters from a real dataset and then set my nCells to 50 as I want to simulate a two-group (each with 25 cells) framework where 10% of genes are DE. This seems to work however in downstream DE packages there are no DE genes detected. Is this something to do in relation with effect size not being large enough for the parameters of the DE packages (DESeq2, DEsingle, MAST etc). Could you advise on a suitable parameter to set my DE genes so that the packages will recognise at least some as being DE? Here are the parameters I have used below in the simulation that have yielded no success and all settings regarding the DE packages are set to default:

splat_parameters_drosophila <- splatter::splatEstimate(drosophila10X)
splat_parameters_drosophila_25cell <- setParam(splat_parameters_drosophila, "batchCells", 50)

sim25 <- splatter::splatSimulateGroups(splat_parameters_drosophila_25cell, 
                                       group.prob = c(0.5,0.5),
                                       de.prob = 0.1,
                                       de.facLoc = 0.3)

Any assistance would be greatly appreciated, thanks! Olympia

splatter • 213 views
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luke.zappia ▴ 50
Last seen 7 months ago

Hi Olympia

Thanks for giving Splatter a go! Hopefully it can be useful for your project.

I can't see any obvious problem with the parameters you have set but it might be helpful to see the other parameters including those that have been estimated by splatEstimate().

The other thing I would suggest you do is visually inspect some of the genes with the biggest/smallest DE factors. Something like a simple box plot should show you if there is something to detect. If there is no obvious difference in expression levels between the groups then you might need to adjust the simulation but if you can see something the problem might be somewhere else (how you are providing the data to the DE methods for example).


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