Hello everyone,

I have a gene expression matrix consisting of 10 genes (rows) and 300 samples (columns). My objective is to prepare this dataset for eQTL analysis.

It is necessary to convert the data into a standard normal distribution when conducting tests on my linear mixed model.

Currently, I am working with TPM as my starting point. Here are the steps I plan to take:

Apply a log transformation to TPM+1 and I intend to perform this operation on a per-gene basis.

Either perform Quantile Normalization or Median Normalization - I believe it would be best to apply this step on a per-sample basis.

Standardize each gene by scaling them so that the mean equals 0 and the standard deviation equals 1.

Can someone confirm if my thought process is correct? Any other comments are welcome.

raw counts are available! I will check the proposed method, thank you for your input!