object 'Cells.in.Well' not found

[deliasoto]

Hello,

I cannot filter cells using: valid_cells <- row.names(subset(pData(HSMM), Cells.in.Well == 1 & Control == FALSE & Clump == FALSE & Debris == FALSE & Mapped.Fragments > 1000000)) I get this message: Error in eval(e, x, parent.frame()) : object 'Cells.in.Well' not found

Do you know why that might be happening? I am running data generated with 10X, and I am using monocle v2.9.

[cswoboda]

Hey Delia,

Cells.in.well is an object placed into the meta data that's used by the tutorial. If you're using your own data, if you don't have that meta data (as in this isn't something found in your count matrix with your cell identities)m then you wont be able to filter the cells using Cells.in.Well, at least this is what I understand.

Hope this helps,

Casey

[naixiangxiaozi]

Hi Casey, But if I import the data from seurat and my pData have nfeature_RNA can I subset the nfeature_RNA parameter as what we can do in the Seurat?