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yizhuo-wang / CASi

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Some bugs discovered during use #3

Open elegantmedstu opened 1 month ago

elegantmedstu commented 1 month ago

Currently, this version of the FindTemporalDEGs.R script seems to only support Seurat 4. The issue occurs at this step:

gene_name = Seurat::GetAssayData(object = expression_filtered, assay = "RNA", slot = "counts")[j,]

Additionally, I found that the glm.nb function does not work correctly in my attempts. A possible modification is as follows: tryCatch({ glm_nb <- MASS::glm.nb( y_2 ~ status + as.numeric(time) + as.numeric(time) * status, data = meta ) })

elegantmedstu commented 1 month ago

For the first question, the possible modification method is: Gene_name <-LayerData (Expression_filter, assay = "rna", layer = "counts") [j,]

https://mp.weixin.qq.com/s/gs-1T2XSDNGWCKMXD7HSPG