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ΔCt / ΔΔCt calculator (relative expression)

Paste qPCR Ct values to calculate ΔCt/ΔΔCt and relative expression (2^-ΔΔCt). Supports calibrator selection, multiple reference genes, Pfaffl efficiency correction, plots, step logs, CSV/LaTeX, and share URLs.

All calculations run in your browser; data is not sent. For research/education use only. Not for diagnostics.

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How to use (3 steps)

  1. Paste data (Group, Sample, Ct_target, Ct_ref) or load a CSV. For multiple references, use Ct_ref1, Ct_ref2, ...
  2. Select a calibrator group (or sample) and summary method (mean/median). Enable Pfaffl correction if needed.
  3. Click Calculate to show ΔCt/ΔΔCt, log2FC, and fold in tables and plots. Share URLs keep the same settings.

Recommended order

  1. First, check efficiency with a standard curve → qPCR standard curve
  2. Next, calculate ΔCt / ΔΔCt (this page)
  3. If needed, assess variability or significance → Confidence interval & hypothesis tests

Go deeper

Data input and options

Defaults are examples. Selecting a preset updates inputs and settings immediately. For your own data, paste and click Calculate.

Results (summary)

Results will appear here.

Per-row results

Row Group Sample Ct_target Ct_ref ΔCt ΔΔCt log2FC fold Outlier

Outliers are not removed automatically; they are shown as candidates (IQR-based).

Group summary

Group n log2FC mean log2FC SD log2FC SEM fold geometric mean fold arithmetic mean

Plots (log2FC / fold)

Calculation steps (How it’s calculated)

    FAQ

    What is the difference between ΔCt and ΔΔCt?

    ΔCt is the within-sample difference between target and reference. ΔΔCt is the difference relative to a calibrator.

    What is the assumption for 2^-ΔΔCt?

    It generally assumes the target and reference amplification efficiencies are equal or similar. Use Pfaffl correction if they differ.

    Should I use fold or log2FC?

    log2FC is symmetric and easier for statistics and plots. Fold is more intuitive.

    How are multiple reference genes handled?

    When Ct_ref1, Ct_ref2, etc. are provided, reference Ct values are aggregated before calculating ΔCt.

    When should I use Pfaffl efficiency correction?

    Consider Pfaffl correction when target and reference efficiencies differ substantially.

    Does the share URL include data?

    Only settings are saved; data are not included.

    References (notes)

    Assumptions and guides on this page are general references. For research/education, consult primary sources as needed.

    Comments

    Share questions or improvements (comments load after you click the button).