Specific factors vary based on global.

[ktroule]

Thanks for creating this tool.

I have a question regarding the definition of global and specific gene sets.

From what I have understood, by definying a specific gene sets we aim to study the within cell type variance of this gene set by applying the matrix decomposition approach only to that cell type, right?

On the other hand, I have done a few test for me to understand the outputs of the method.
I have generated two gene set collections for spectra inputs:

1. As global the hallmark gene sets collection (50 gene sets) from MSigDB and 15 specific gene sets for two specific cell types.
2. As global the ~180 cytopus "all_" starting gene sets and the same 15 specific gene sets for the same two cell types.

I've found that when checking the output values for those specific gene sets there were noticeable differences. That makes me think that differences in the global gene sets will affect results for the specific gene sets, right?

Can you give a hint on how to better choose global gene sets or the rational behind their selection?

Thanks!

[christophechu]

Same question：
Can you give a hint on how to better choose global gene sets or the rational behind their selection?
How to choose the best global gene sets.