| Criteria | Microarray | RNA-Seq | Remarks |
| Principle | Hybridization of labeled cDNA to known probes on a chip | Sequencing of cDNA to capture transcriptome-wide information | Microarray relies on pre-designed probes; RNA-seq captures de novo sequences |
| Detection Scope | Detects only known transcripts with available probes | Detects both known and novel transcripts, including splice variants | RNA-seq has broader detection capabilities |
| Quantification | Relative quantification based on hybridization signal | Absolute and relative quantification based on read counts | RNA-seq provides more accurate dynamic range |
| Sensitivity & Specificity | Lower sensitivity; background noise due to cross-hybridization | High sensitivity and specificity | RNA-seq is more reliable for low-abundance transcripts |
| Data Output | Fluorescence intensity values | Sequencing reads (raw reads and transcript counts) | RNA-seq produces large datasets with higher complexity |
| Dynamic Range | Limited dynamic range | Broad dynamic range | RNA-seq can detect subtle changes and rare transcripts |
| Cost and Accessibility | Generally less expensive; requires specific array design | Higher initial cost; decreasing over time | RNA-seq more accessible with improved sequencing platforms |
| Applications | Gene expression profiling, genotyping, comparative expression | Transcriptome profiling, isoform detection, mutation and SNP analysis | RNA-seq offers greater functional insights beyond expression profiling |
