I'm trying to apply Capybara to annotate cells in data that I have from a single tissue.
I followed steps 1-6, where in step5 I only loaded the MCA file from the specific tissue I produced my data from.
The MCA data I used from the link you provide are the MCA_BatchRemove_dge.zip, where the counts files are data.frame's where each row is a gene name and each column is a cell name (and the values are the integer counts).
The file that Capybara generates at the end pf step 5 (after running single.round.QP.analysis, which ends with scale.csv) did not retain the cell names (hence they are V2, V3..) and so in step 6, the intersect(rownames(mca.meta), rownames(curr.qp.rslt)) step results with 0 cells.
Hi,
I'm trying to apply Capybara to annotate cells in data that I have from a single tissue. I followed steps 1-6, where in step5 I only loaded the MCA file from the specific tissue I produced my data from. The MCA data I used from the link you provide are the MCA_BatchRemove_dge.zip, where the counts files are
data.frame's where each row is a gene name and each column is a cell name (and the values are the integer counts). The file that Capybara generates at the end pf step 5 (after runningsingle.round.QP.analysis, which ends withscale.csv) did not retain the cell names (hence they areV2,V3..) and so in step 6, theintersect(rownames(mca.meta), rownames(curr.qp.rslt))step results with 0 cells.Can you please advise?
Thanks!