ctQc: Quality Control Filter for Replicate Ct Values
In qpcrNorm: Data-driven normalization strategies for high-throughput qPCR data.

Description Usage Arguments Details Value Author(s) See Also Examples

This function applies a quality control filter to triplicate Ct values before combining them into a single summary Ct measure.

Current implementation can only handle three replicates.

ctQc(x)

`x`	Matrix with three columns, corresponding to the triplicate Ct values.

Applying ctQc is an alternative to averaging the triplicate Ct values. This filter was originally developed by Yasumasa Kimura 1. For each primer, sort Ct values in ascending order so we have [ct1, ct2, ct3]. 2. Take two differences difference1 := ct2 - ct1 difference2 := ct3 - ct2 If either or both have ct 40, we don't calculate the difference and set it to region 4 in the next step. 3. Take an average according to the differences. Here we have 2 thresholds : 0.2 and 1.0. With the thresholds, we classify the 2 differences into the below regions. region1 : difference <= 0.2 region2 : 0.2 < difference <= 1.0 region3 : 1.0 < difference region4 : either or both ct are 40 If the 2 differences are in same region, we take an average of 3 ct values. If the 2 differences are in different regions, we take an average of 2 ct values which are in smaller number region.

Numeric vector of Ct values combined over the three replicates according to the QC filter.

Yasumasa Kimura
Jess Mar jess@jimmy.harvard.edu

readQpcr, readQpcrBatch