maddygriz
commented
2 years ago Hi Austin,
Sorry for the slow response.
These profile matrices were generated using outside data so I'm not sure exactly what the macrophage labels indicate or if M1 would be part of that. I believe that this dataset was generated from this paper, https://www.nature.com/articles/s41586-020-2157-4, but we lost some of the metadata since these have been processed so I cannot be 100% positive.
However, I would suggest using a different profile matrix if you are only looking into the immune population. The Human_Cell_Landscape is a wide dataset that will increase runtime significantly and you will have results not pertinent to your study. We have updated profiles in the NewProfileMatrices branch if you want to take a look at those but I don't know if we have a great dataset for macrophage differentiation. The ImmuneCensus_HCA dataset would be good for T cell activation but it, unfortunately, doesn't have a profile for macrophages.
The newest version of SpatialDecon (v1.4), does have a function to create a custom profile matrix from any single cell dataset if you find a paper that you want to use.
Hope that helps, Maddy
Hi,
I was looking at the Human_Cell_Landscape file and do not understand the differences between the different macrophage annotations. I saw a M2 macrophage annotation but not an M1 - do one of the other macrophage labels correspond to M1 macrophages? Is there a difference in function or activation level between the other macrophage lables?
I am hoping to use the matrix to look at immune populations and function, specifically macrophage and T cell activation and exhaustion and wanted to make sure I'm fully understanding the different categories.
Thank you so much! Austin