Too Many Results: RNA-seq often detects numerous changes in gene expression, making it hard to separate meaningful data from technical noise.

Snapshot Limitation: The transcriptome reflects gene expression at a single moment in time, which may not fully capture dynamic changes.

Tissue Relevance: It's essential to study the right tissue or cell type related to the disease or condition, or the data might not be meaningful.

Time Sensitivity: Gene expression can vary over time, during different stages of development, or under disease conditions, complicating analysis.

Cell-Type Variation: Different cell populations within a sample can react differently to treatments, potentially obscuring results.

Validation Needed: While RNA-seq shows differential expression, it doesn't explain why these changes occur, requiring follow-up studies for confirmation.

Spell: Using the Results of Genetic Studies (Genomics)