guescini

{guescini} is an R data package that provides real-time PCR raw fluorescence data by Guescini et al. (2008) in tidy format.

Installation

Install {guescini} from CRAN:

# Install from CRAN
install.packages("guescini")

Data

Guescini et al. (2008) explored the effect of amplification inhibition on qPCR quantification. Two systems were devised to alter the amplification efficiency:

• decreasing of the amplification mix used in the reaction
• increasing of IgG (PCR inhibitor) concentration in the reaction

The raw fluorescence data associated with the decreasing of the amplification mix is provided as the data set amp_mix_perc; the data obtained with increasing concentrations of IgG is provided as IgG_inhibition.

Amplification mix percentage

The data set amp_mix_perc corresponds to a set of amplification runs where the MT-ND1 gene is amplified in reactions having the same initial amount of DNA but different amounts of SYBR Green I Master mix. A standard curve was performed over a wide range of input DNA ($3.14 \times 10^7\ \text{thru}\ 3.14 \times 10^1$) in the presence of optimal amplification conditions (100% amplification mix), while the unknowns were run in the presence of the same starting DNA amounts but with amplification mix quantities ranging from 60% to 100%.

library(guescini)
amp_mix_perc
#> # A tibble: 21,000 × 12
#>    plate well  dye   target sample_type run   replicate amp_mix_perc   copies
#>    <fct> <fct> <fct> <fct>  <fct>       <fct> <fct>            <dbl>    <int>
#>  1 <NA>  <NA>  SYBR  MT-ND1 std         1     1                    1 31400000
#>  2 <NA>  <NA>  SYBR  MT-ND1 std         1     1                    1 31400000
#>  3 <NA>  <NA>  SYBR  MT-ND1 std         1     1                    1 31400000
#>  4 <NA>  <NA>  SYBR  MT-ND1 std         1     1                    1 31400000
#>  5 <NA>  <NA>  SYBR  MT-ND1 std         1     1                    1 31400000
#>  6 <NA>  <NA>  SYBR  MT-ND1 std         1     1                    1 31400000
#>  7 <NA>  <NA>  SYBR  MT-ND1 std         1     1                    1 31400000
#>  8 <NA>  <NA>  SYBR  MT-ND1 std         1     1                    1 31400000
#>  9 <NA>  <NA>  SYBR  MT-ND1 std         1     1                    1 31400000
#> 10 <NA>  <NA>  SYBR  MT-ND1 std         1     1                    1 31400000
#> # ℹ 20,990 more rows
#> # ℹ 3 more variables: dilution <int>, cycle <int>, fluor <dbl>

amp_mix_perc %>%
  ggplot(mapping = aes(
    x = cycle,
    y = fluor,
    group = interaction(run, amp_mix_perc, copies),
    col = format(copies, big.mark = ",", scientific = FALSE)
  )) +
  geom_line(linewidth = 0.2) +
  geom_point(size = 0.2) +
  labs(y = "Raw fluorescence", colour = "No. of copies", title = "Seven-point 10-fold dilution series amplification mix percentage") +
  guides(color = guide_legend(override.aes = list(linewidth = 0.5), reverse = TRUE)) +
  facet_wrap(vars(amp_mix_perc))

Inhibition by IgG

The data set IgG_inhibition provides those runs performed in the presence of an optimal amplification reaction mix added with serial dilutions of IgG (0.0 - 2 ug/ml) thus acting as the inhibitory agent.

IgG_inhibition %>%
  ggplot(mapping = aes(
    x = cycle,
    y = fluor,
    group = interaction(IgG_conc, replicate),
    col = paste(as.character(IgG_conc), "ug/ml")
  )) +
  geom_line(linewidth = 0.5) +
  geom_point(size = 0.5) +
  labs(y = "Raw fluorescence", colour = "IgG concentration", title = "Serial dilutions of IgG (PCR inhibitor)") +
  guides(color = guide_legend(override.aes = list(linewidth = 0.5)))

Code of Conduct

Please note that the guescini project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

References

Michele Guescini, Davide Sisti, Marco BL Rocchi, Laura Stocchi and Vilberto Stocchi. A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition. BMC Bioinformatics 9:326 (2008). doi: 10.1186/1471-2105-9-326.