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Teichlab / cellphonedb

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How to interpret negative log2 means in dot plot #230

Open hemadelon opened 3 years ago

hemadelon commented 3 years ago

Hi guys,

I performed the statistical analysis on a merged dataset. This merged dataset was preprocessed as follows: I had one dataset containing stromal cells and one dataset containing T cells (both Seurat objects). I merged the countmatrices and performed SCTransform. The outcomes of this normalization step were used as imput of CellphoneDB.

What I observed are a lot of interaction pairs with means below 1 (but above zero). However, in the dotplot (where values are log2 transformed) these obviously become negative.

Are these findings then still biologically relevant? Since I do find differences between clustercouples than would fit my hypotheses, but I'm puzzled by the low mean + negative log2 result.

Best, Madelon

rgranit commented 3 years ago

+1

shexiaolu commented 3 years ago

+1