I wanted to create pseudo-bulk samples, and instead of doing it by hand, I looked into the aggregate_gene_expression() function, in hopes it would get the job done. However, this function forces normalization (what probably makes sense for its usual applications).
I found a workaround to acutally use this function to create pseudo-bulk counts:
However, an implementation of something like norm_method = "none", would solve the issue of having to change the size factors.
I know, pseudo-bulk anaylsis is not part of the complete monocle workflow. But it could be useful for people, who like to use monocle for some parts of their analysis, like me.
Hi,
I wanted to create pseudo-bulk samples, and instead of doing it by hand, I looked into the
aggregate_gene_expression()function, in hopes it would get the job done. However, this function forces normalization (what probably makes sense for its usual applications).I found a workaround to acutally use this function to create pseudo-bulk counts:
However, an implementation of something like
norm_method = "none", would solve the issue of having to change the size factors. I know, pseudo-bulk anaylsis is not part of the complete monocle workflow. But it could be useful for people, who like to use monocle for some parts of their analysis, like me.