I have a bulk RNA-seq dataset from a PBMC mixture that I want to deconvolute using the reference matrix from Monaco et al 2019. However, I've noticed that only half of the genes in the Monaco reference matrix are present in my dataset. I used the AnnotationDbi package to compare Ensembl IDs between the two datasets.

1. How can I improve or fix the gene matching issue between my bulk RNA-seq data and the Monaco reference matrix?
2. How might these discrepancies affect the accuracy of the deconvolution using the CIBERSORT protocol?
3. Are there any recommended strategies or tools to handle missing genes or improve the overlap?

Any insights or suggestions would be greatly appreciated!

Code should be placed in three backticks as shown below

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )