Docs · Guide step 3

Setting CT cutoffs.

Step three of the first-report guide, and the most common place a new lab pauses. Two bounds per target: where the numbers come from, what a filled-in panel looks like, and why they arrive blank on purpose.

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Two bounds, one window

The guide’s own wording: “Every target needs a Lower and Upper CT — the window that reads as positive. Open your panel and fill both bounds for each target.” At run review, each target’s Ct is read against its window. Filling both bounds for a panel takes about a minute; the judgment behind the numbers stays yours.

What a filled panel looks like

Target	Channel	Lower CT	Upper CT
Escherichia coli	FAM	12	37
Klebsiella pneumoniae	HEX	13	36
Enterococcus faecalis	ROX	14	37

Why the catalogue hands them to you blank

Import a pathogen from the shared catalogue and its identity comes across whole — name, type, disease caused, gram stain. Instrument name, channel, lower CT, upper CT and load value arrive empty; the first four become required on your copy before you can run it, and the load value stays your call. Copying them across would look like an answer while being a guess about somebody else’s instrument, and a CT window guessed wrong is a wrong clinical result. Your QuantStudio 5 is not our QuantStudio 5.

instrumentName
channel
lowerCt
upperCt
loadValue

So the bounds come from your lab’s validation of the assay on your instrument — the windows you verified, entered once per target on your copy of the panel.

Load values are opt-in, and the tiers are yours too

Load reporting is switched on per target. Tiers are named rows, each with CT cutoffs of its own — the defaults are 100K, 50K, 10K and 5K, a target needs at least three tiers, and the characterised range runs 5K to 100K. Leave load reporting off and the report prints without it.

Who changed a cutoff, and when

CT cutoffs are controlled records: every change carries an audit trail naming who made it and when. If a bound moves between validations, the record says so — which is exactly what you want on the table when an assessor asks.

Asked before, answered here

Can you suggest a starting window for my target?

No. A window we shipped would look like an answer while being a guess about your instrument. The software’s job is to require both bounds and record who set them; the numbers come from your validation runs.

What happens while a bound is still blank?

The field is required on your lab’s copy, and the first-report guide deep-links to the exact panel still missing one — the gap is named up front rather than discovered at release.

Do the demo panels count?

No. Seed and demo rows never tick a guide step — a tweaked demo panel is not your lab’s panel.

Your panels are one screen away.

Open a panel, fill both bounds on each target, and step three ticks itself off.

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Open your panels →

Unsure about a window: support@pcrlabpro.com.