EPIC

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Confusion about correlation between EPIC and MCPcounter

2

Hi, David I perform EPIC analyses on BRCA and OV RNASeq data from TCGA these days. It confuses me when I run MCPcounter (another method, https://github.com/ebecht/MCPcounter), the results of these...

leleye

Can EPIC accept CPM or microarray data?

1

Hi there, It looks like EPIC is designed for RNA-Seq TPM data. Is RNA-Seq CPM data ok? How about fitting microarray data into EPIC? If possible, is any normalization (like...

thelingxichen

mRNA_cell value unknown for some cell types: CAFs, Endothelial...

1

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...

bhinderb

Adding TRef and BRef references

1

Hello, Thank you for developing this useful tool to identify cell fractions in tumor cells. I have already used the tool using reference datasets and I do get some useful...

kgaonkar6

Can we used normalised counts as input?

1

Hi. I'm keen to use EPIC and read in the instructions that it only accepts TPMs or FKPMs. Is it possible to use normalised counts instead? Thanks.

guray003

ATAC-seq deconvolution

1

Dear, Is it possible to use EPIC for cell type deconvolution using ATAC-seq datasets? It gives the following error when I provide bulk ATAC-seq matrix (rows=peaks, columns=sample/subject) as input. Error...

seoyeonoh12