Clinical Data Analysis, Should compared with Normal tissue?

Question

[bxia]

Just curious about how to compare RNA-seq data from clinical patient.

I saw an old tutorial post, which transform all data to Z-score,

Just curious, based on that conversion, we are looking at def expression genes with normal tissue, not the gene with high expression or low expression within the tumor sample.

Is it a standard that all the data should be normalized with their control sample?

Thanks

[russhh]

It's very rare to compare RNA-seq data using Z-scores for the purposes of differential expression. Typically you'd use DESeq2, edgeR or voom (or one of a number of other similar tools), for which the input is raw read counts

Answer 1

[bxia]

And when we define a type cancer, let's say ER+, the conclusion we drew is solely from tumor sample, not comparison, right? Then in this case, why should we transform the data to Z-score.