Subsetting AUCmatrix; Understanding the output after pruning

[saeedfc]

Hi,

Thanks for the amazing tool.
I have a few doubts regarding the output. I really appreciate your help on these.

1. I have a dataset that has been integrated with Seurat v3. Can I use a normalized matrix from the integrated seurat object for SCENIC? Or do you suggest running on raw matrix of each 10x run separately(Between the runs, there could be some depth difference, the samples aren't the same as they are different phases of inflammation)? In that case what would be your suggestion to combine the data?

2)If I derive AUCELL matrix for an expression matrix of n cells, Can I still use the same AUCELL matrix to work with a subset of the data (say m cells, m<n) ? Or do I have to rerun SCENIC for the subset of m cells of the data separately? (Asking because I don't know whether there is any pan data normalization or dependency generated internally in the workflow),

I have a dataset of all immune cells and later in the study I focus on myeloid cells. Hence the question

3)After pruning we obtain a data frame with the transcription factor and their targets. In paranthesis of each target gene, a value is given. What is this value?

Thanks again!