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GfellerLab / EPIC

Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
https://gfellerlab.shinyapps.io/EPIC_1-1/
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mRNA_cell value unknown for some cell types: CAFs, Endothelial... #10

Closed bhinderb closed 1 year ago

bhinderb commented 2 years ago

Hi - I get a warning message when running EPIC (input dataset is TCGA RNAseq FPKM). Please advise on a resolution.

Warning message: In EPIC(bulk = bulkSamplesMatrix) : mRNA_cell value unknown for some cell types: CAFs, Endothelial - using the default value of 0.4 for these but this might bias the true cell proportions from all cell types.

jracle85 commented 2 years ago

Hello, This is indicated in the the FAQ part of the README: https://github.com/GfellerLab/EPIC#what-is-the-meaning-of-the-warning-message-telling-that-some-mrna_cell-values-are-unknown Best regards, Julien