Summary: an example 96-well qPCR experiment. | Setup knitr options and load packages | Loading, organizing, and sanity-checking data. | Load data from machine output file | Organize sample and target data on the plate | Display the plate layout | Plot unnormalized Cq data | Normalized data: delta Cq | Normalize Cq to 5S rRNA, within Sample only | Plot normalized data, all reps | Calculate a summary value for each sample-target combination | Plot delta Cq for each OD separately across genes | Plot relative abundance for each OD separately across genes | Plot relative abundance for each gene separately across ODs | Doubly normalized data: delta delta Cq | Calculate delta delta cq against a chosen reference sample | Plot delta delta Cq (log2-fold change) for each target gene | Plot fold change for each target gene | Conclusion | Notes on normalization, reference targets, and reference samples

Summary: an example multifactorial qPCR experiment. | Pilot experiment | Setup knitr options and load packages | Label and plan plates | Load and summarize data | Plot unnormalized data | -RT controls are low | Normalize Cq to PGK1, within Sample only | Plot normalized data, all reps | Plot normalized data, summarized vs target_id | All on same axes | Faceted by drug treatment | Faceted by heat shock condition | Melt and Amplification Curves | Melt Curves, biol_rep 1 | Melt Curves, biol_rep 2 | Amp Curves, biol_rep 1

Summary: calibrating primer sets from a real experimental test | Setup knitr options and load packages | Set up experiment | Describe which primer set we put in which well using a row key | Combine the row key describing primer sets with column key describing on samples and dilutions. | Spot-check the plate plan | Display the plate plan | Analyse Cq (quantification cycle count) data | Load and summarize data | Visualise Cq values for each well. | Plot unnormalized data shows that -RT and NT controls are low | Dilution series is linear for all probes | Calculate primer efficiencies for all probes | Dilution series for nice probes only shows linearity clearly | Analyse amplification and melt curve data | Load raw data for amplification and melt curves. | Plot de-baseline'd raw data for single well | Plot all amplification curves | Plot melt curve for single well | Plot all melt curves | Plot zoomed melt curves | Plot only zoomed melt curves for nice probes | Conclude acceptable primer sets

Overview | Setup knitr options and load packages | Essential information: target_id, sample_id, prep_type | Using rows and columns to make life easier | A Minimal 48-well plate plan | Practice version, only a single technical replicate. | Replicate columns for the sample_ids and prep_types | Putting the 48-well sample together | Adding more samples and repeating targets | Adding experimental conditions | Repeating target names without repeating yourself | Recreating the column key | Combining information into a larger plate plan | Making sure sample names are present and unique | Creating plate layouts with standard designs | What information goes in the plate plan, revisited? | Hints and Tips on Plate setup