Normalize RNA seq data from multiple runs for expression analysis
There are a number of methods. If you're doing DE, you have ComBatSeq, SVAseq, RUVseq, BUSseq. You could also try Z-score normalization ($(x - \overline{x}) / \sigma$) or even quantile transformation. For the latter two, make sure you work on each batch individually, not the whole dataset at once. See more on that here.
To visually compare if transformation works, plotting PCA/UMAP/t-SNE on raw and transformed data can perhaps be of some insight.