Trouble achieving final matrix for MCPcounter with mouse bulk RNAseq

[lauraramirezfinn]

Hello,

We are trying to use MCP counter on mouse bulk RNA seq data.

First we tried mMCPcounter, however we encountered issues with their given signature.

So, next, we tried MCPcounter. We have our expression data with ENSEMBL_ID as rownames. We have tried running MCPcounter.estimate with your given probesets and genes from Github. However, this returns a 0 x 0 matrix.
Next we tried, using our own immune signatures. This returns a matrix with our immune cells as row names and samples as column names, but no values, instead the matrix is full of NA.
This is what we are running: EST_custom <- MCPcounter.estimate(expressionData4,
featuresType=c("ENSEMBL_ID")[1],
genes= custom_signatures)

We were wondering if this works with ENSEMBL_ID for mice or just for human in this function?

Any help would be greatly appreciated as immunologists who are learning bioinformatics!! Thank you

[ebecht]

Hello,
The package is designed for human data. Colleagues have developed an alternative for mouse data : https://doi.org/10.1186/s13073-020-00783-w
Best,
Etienne