Compare cell proportions across samples

[xi11]

Hi,

Thanks for the great tool, it's very useful!

We have been using spaCET for a project with 10 Visium samples, running per sample. I just want to double check if the cell% could be compared across samples. From what I've understood, as malignant% and major lineage cell% (including unidentified%) are added up to 100, then these cell% represent absolute value, thus deconvolved cell proportions can be comparable across samples. Am I understanding correctly?

Best,
Xiaoxi

[beibeiru]

Hi @xi11,

When using the in-house reference, we do not recommend comparing inferred cell proportions across samples, as the malignant prediction is based on relative values within each individual sample.

Best,
Beibei

[beibeiru]

I recommend analyzing each sample individually using SpaCET, and then summarizing the results by calculating the mean (or other statistics) across all samples.

Best,
Beibei

[xi11]

I see. we did apply SpaCET to each sample individually.

1. so as long as I took/compare inferred cell proportions within each sample for downstream analysis, it should be fine right?
2. if I have tumor cell% derived from H&E image per spot, then I should be able to rescale TME cell proportions inferred from SpaCET to absolute mode, something like TME_abs = TME_spacet/(1-Malignant) * (1-tumor_cell_proportion_h&e)? Then cell proportions should be comparable across samples.

Xiaoxi

[beibeiru]

1. Yes.
2. I am not sure, as I currently do not have the benchmark data to verify it.

Best,
Beibei