REF matrix scale

[onsamoylova]

Can I ask you a question about reference scale for the Insitutype cell labeling part? From https://github.com/Nanostring-Biostats/InSituType/blob/main/vignettes/NSCLC-supervised-cell-typing-vignette.Rmd It mentioned:

4. A "reference matrix" giving the expected expression profile of each cell type, with genes in rows and cell types in columns. The reference matrix must be in linear-scale, not log-scale. And they used reference matrix in linear scale , provided as a part of the package:

data("ioprofiles")

From other side on nanostring tutorial: refprofiles <- read.csv(https://raw.githubusercontent.com/Nanostring-Biostats/CosMx-Cell-Profiles/main/Human/IO/IO.profiles.csv, row.names = 1, header = TRUE)

which is a log scale(?)

Could you please verify what scale of ref matrix should be used. Log vs linear scale give different results.

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