Hello, I am using Seurat for single cell RNA-seq analysis of drosophila data. After I did cell level filtering, I tried gene level filtering as below. However, there was an error message "Some cells in meta.data not present in provided counts matrix" and there were a lot of "N/A" in the meta.data of filtered_fly9. I would appreciate it if someone could let me know how to fix this.
#Cell level filtering
filtered_fly9 <- subset(x = fly9, subset= log10GenesPerUMI > 0.80)
I confirmed that the metadata of the filtered_fly9 after the cell level filtering was filled in numbers.
#Gene level filtering
counts9 <- GetAssayData(object = filtered_fly9, slot = "counts")
nonzero9 <- counts9 > 0
keep_genes9 <- Matrix::rowSums(nonzero9) >= 10
filtered_counts9 <- counts[keep_genes9, ]
filtered_fly9 <- CreateSeuratObject(filtered_counts9, meta.data = filtered_fly9@meta.data)
There were a lot of "N/A" in the meta.data of the filtered_fly9.
1 answer
You can check that colnames(counts) match rownames(filtered_fly9@meta.data) -- but more generally you do not need to create an entirely new Seurat object to do this. You can go with:
filtered_fly9 <- subset(fly9, ...)
filtered_fly9 <- filtered_fly9[rowSums(GetAssayData(filtered_fly9, 'counts') > 0) > 10,]
which should eliminate the error.
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Hello Dr. tomas4482, thank you so much for your message. Now I understand why there were a lot of N/A... I appreciate your taking time.
Why did you delete your posts? Who's Dr. tomas4482?
I think my original answer should be something like:
But later I found that the count assay seems to subset genes only. The answer may be incorrect. Without an test sample, I'm not able to find out the reason. Therefore, I deleted the original answer.
I see. I think it was done pretty quickly, as moderators such as myself are able to view deleted posts for a while. I'll delete this thread in a bit.