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drisso / zinbwave

Clone of the Bioconductor repository for the zinbwave package, see https://bioconductor.org/packages/zinbwave
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zinbwave on integrated data set #62

Closed yeroslaviz closed 4 years ago

yeroslaviz commented 4 years ago

I would like to better understand how to apply the zinbwave workflow onto my integrated data set.

I have four datasets, from two different conditions in replicates. In Order to first find the most variable genes i have done in seurat the standard workflow and used the SCTransform as well as the integrateData step to combine the four sets in to seurat object.

Now O would like to test try to apply the zinbwave method to the data and find differential expressed genes between my two conditions.

Would it makes more sense to re-run the complete workflow from the beginning or maybe it is better to take the genes seurat has found to be variable after the integration (with FindVariableFeatures).

thanks

Assa

drisso commented 4 years ago

Starting from Seurat's most variable genes is probably what I would do (at least as a first pass) since you already have them.

I would bother going back from the beginning only if the results of zinbwave are unexpected.