Quality Control
Automated QC pipeline
AnnealIQ runs quality checks automatically after data parsing. If issues are found, a collapsible QC summary card appears with findings sorted by severity: errors first, then warnings, then informational items.
Each finding has actionable buttons: Exclude (remove the flagged replicate from analysis) or Keep (acknowledge and continue). When all checks pass, a single green "All QC checks passed" card appears.
What’s checked
| Check | Severity | What it detects |
|---|---|---|
| Technical replicate outliers | Warning | Grubbs’ test flags statistical outliers |
| Missing/zero Ct values | Error | Wells with no amplification data |
| Insufficient replicates | Warning | Fewer than 3 technical replicates |
| Reference gene instability | Warning | M-value above stability threshold |
| Abnormal fold-change | Warning | Very large or very small fold changes |
| NTC contamination | Error/Warning | Template detected in no-template controls |
| NRT contamination | Error/Warning | Genomic DNA detected in no-RT controls |
NTC/NRT control well interpretation
AnnealIQ auto-detects No-Template Control (NTC) and No-Reverse-Transcriptase (NRT) wells from RDML sample type metadata or sample name patterns (word-boundary matching: "NTC", "No Template", etc.).
HIGH severity (error): NTC/NRT Ct is within 5 cycles of sample Ct — contamination likely. The finding shows the specific Ct values and gap.
MEDIUM severity (warning): Detectable amplification but distant from samples — possible primer dimers. The AI suggests investigation.
INFO: Clean controls — no contamination detected.
NRT findings include a specific explanation of genomic DNA contamination with primer-spanning-intron guidance. When multiple control wells exist for one target, the worst case (lowest Ct) is reported.