Category Archive: Bioinformatics

Nov
27

FDA Validation of a PCR test: Accuracy (Part 4)

In the Accuracy study, we will: Set the acceptable working range Set the cutoffs for calling a sample positive or negative Assess how well our assay agrees with an alternative assay Clinical samples can  be FFPE or fresh frozen. FFPE is usually poorer quality than fresh frozen, so the two sample types are treated separately. …

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Nov
27

FDA Validation of a PCR test: Analytical Specificity (Part 3)

Analytical specificity shows how robust the test is to contamination. Positive controls with the fusion were spiked with EDTA or ethanol at various concentrations. We determined at which concentration the PCR no longer worked. The figures and results in this blogpost were generated by R code corresponding to “AnalyticalSpecificity_R_scripts.txt” on github Pictures always help, so these …

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Nov
27

FDA Validation of a PCR test: Pre-processing data (Part 2)

All of the data analyzed used the same format to make it easy to re-use code . The data for each PCR experiment was in an Excel file or a comma-delimited (.csv) file with the following format. To be able to complete the FDA sections above, data from the different runs need to be combined …

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