I'm trying to assess the gene expression correlation between a specific gene and all other genes, thanks to a public scRNA seq dataset of human melanoma biopsies.(https://singlecell.broadinstitute.org/single_cell/study/SCP109/melanoma-immunotherapy-resistance#study-summary)
For this I perform a spearman correlation test on the tpm values, after filtering the samples to keep only the cells where my gene is expressed. However I'm only getting low correlation (all under 0.25), and I'm wondering why.
According to you, is low correlations necessarily expected ? (due to the low sensitivity of scRNAseq ? )
Would anyone know highly correlated housekeeping genes that I could use as positive controls ?
Thank you for any input