Normalization for RNA-Seq samples

Question

[ATCG]

Hi I want to extract genes that are expressed in a tissue-specific manner, not expressed, expressed across tissues. I am working with RNA-Seq data across different tissues.

I’m sure others have done this experiment already. I have the following questions:

1. I will start with a counts table, output of featureCounts, how would I normalize samples, usually I would use DESeq2, but in this case, I am not using DESeq2. (I will have data generated in different batches, labs, library size, technical variation.)

2. What is an appropriate threshold for expressed vs. non-expressed, and can this information be derived accurately from RNA-seq data.

I hope this makes sense. Best!