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Pk/Pv/Pf Serology Tutorial

Source: vignettes/Pk_Pv_Pf_Serology_Tutorial.Rmd
Pk_Pv_Pf_Serology_Tutorial.Rmd

For all of these analyses you can run as many plates as you wish.

Visualisation of the Pk/Pv/Pf Pipeline

5-Point Standard Curve

Step 1: Load your data!

Firstly, we will be using our example data that’s in-built in the package. Here replace the system.file() argument with the file path for your package.

your_raw_data_5std <- c(
  system.file("extdata", "example_MAGPIX_pk_5std_plate1.csv", package = "SeroTrackR"),
  system.file("extdata", "example_MAGPIX_pk_5std_plate2.csv", package = "SeroTrackR")
)
your_plate_layout_5std <- system.file("extdata", "example_platelayout_pk_5std.xlsx", package = "SeroTrackR")

Step 2: Read your data and process MFI to RAU

This function to (a) process raw Serological data and (b) convert MFI to RAU. The runPlasmoPipeline() function will output three data frames:

  1. All_Results: All columns of every MFI to RAU conversion
  2. MFI_RAU: Just the SampleID, Plate, MFI and RAU values per antigen
  3. MFI_RAU_long: SampleID, Plate, MFI, RAU, Antigen, Species (long-format df)
results_5stdcurve <- runPlasmoPipeline(
  raw_data = your_raw_data_5std,
  platform = "magpix",
  plate_layout = your_plate_layout_5std,
  panel = "panel1",
  std_point = 5, 
  experiment_name = "5-point standard curve"
)
#> PASS: File example_magpix_pk_5std_plate1.csv successfully validated.
#> PASS: File example_magpix_pk_5std_plate2.csv successfully validated.
#> Plate layouts correctly identified!
#> QC Processes completed.
#> QC Plotting completed.
#> MFI to RAU conversion completed.
#> Pv classification completed.
Standard Curve Plot 
results_5stdcurve$std_curve

Bead Counts QC Plot 
results_5stdcurve$bead_counts

Blanks QC Ploat 
results_5stdcurve$blanks

MFI to RAU Tables

All results:

results_5stdcurve$mfi_outputs$All_Results %>%
  head() %>% 
  kable()
SampleID Location Location.2 Sample Plate Pk8_MFI Pk8_log_mfi Pk8_max_s1 Pk8_max_dil Pk8_slope Pk8_low_asym Pk8_upp_asym Pk8_ed50 Pk8_asym_par Pk8_Dilution PkMSP10_MFI PkMSP10_log_mfi PkMSP10_max_s1 PkMSP10_max_dil PkMSP10_slope PkMSP10_low_asym PkMSP10_upp_asym PkMSP10_ed50 PkMSP10_asym_par PkMSP10_Dilution PkSERA3Ag2_MFI PkSERA3Ag2_log_mfi PkSERA3Ag2_max_s1 PkSERA3Ag2_max_dil PkSERA3Ag2_slope PkSERA3Ag2_low_asym PkSERA3Ag2_upp_asym PkSERA3Ag2_ed50 PkSERA3Ag2_asym_par PkSERA3Ag2_Dilution PkSSP2_MFI PkSSP2_log_mfi PkSSP2_max_s1 PkSSP2_max_dil PkSSP2_slope PkSSP2_low_asym PkSSP2_upp_asym PkSSP2_ed50 PkSSP2_asym_par PkSSP2_Dilution QC_total Pv-fam-a_MFI Pv-fam-a_loglog_Dilution Pv-fam-a_DilutionReciprocal Pv-fam-a_MinStd Pv-fam-a_MaxDilution Pv-fam-a_MaxStd Pv-fam-a_MinDilution PvMSP5_MFI PvMSP5_loglog_Dilution PvMSP5_DilutionReciprocal PvMSP5_MinStd PvMSP5_MaxDilution PvMSP5_MaxStd PvMSP5_MinDilution PvMSP1-19_MFI PvMSP1-19_loglog_Dilution PvMSP1-19_DilutionReciprocal PvMSP1-19_MinStd PvMSP1-19_MaxDilution PvMSP1-19_MaxStd PvMSP1-19_MinDilution PvEBP_MFI PvEBP_loglog_Dilution PvEBP_DilutionReciprocal PvEBP_MinStd PvEBP_MaxDilution PvEBP_MaxStd PvEBP_MinDilution PvRBP2b_MFI PvRBP2b_loglog_Dilution PvRBP2b_DilutionReciprocal PvRBP2b_MinStd PvRBP2b_MaxDilution PvRBP2b_MaxStd PvRBP2b_MinDilution PvCSS_MFI PvCSS_loglog_Dilution PvCSS_DilutionReciprocal PvCSS_MinStd PvCSS_MaxDilution PvCSS_MaxStd PvCSS_MinDilution PvPTEX150_MFI PvPTEX150_loglog_Dilution PvPTEX150_DilutionReciprocal PvPTEX150_MinStd PvPTEX150_MaxDilution PvPTEX150_MaxStd PvPTEX150_MinDilution PvMSP8_MFI PvMSP8_loglog_Dilution PvMSP8_DilutionReciprocal PvMSP8_MinStd PvMSP8_MaxDilution PvMSP8_MaxStd PvMSP8_MinDilution PfMSP1-19_MFI PfMSP1-19_loglog_Dilution PfMSP1-19_DilutionReciprocal PfMSP1-19_MinStd PfMSP1-19_MaxDilution PfMSP1-19_MaxStd PfMSP1-19_MinDilution PfAMA1_MFI PfAMA1_loglog_Dilution PfAMA1_DilutionReciprocal PfAMA1_MinStd PfAMA1_MaxDilution PfAMA1_MaxStd PfAMA1_MinDilution Pfetramp5Ag1_MFI Pfetramp5Ag1_loglog_Dilution Pfetramp5Ag1_DilutionReciprocal Pfetramp5Ag1_MinStd Pfetramp5Ag1_MaxDilution Pfetramp5Ag1_MaxStd Pfetramp5Ag1_MinDilution PfHSP40Ag1_MFI PfHSP40Ag1_loglog_Dilution PfHSP40Ag1_DilutionReciprocal PfHSP40Ag1_MinStd PfHSP40Ag1_MaxDilution PfHSP40Ag1_MaxStd PfHSP40Ag1_MinDilution PfGexp18_MFI PfGexp18_loglog_Dilution PfGexp18_DilutionReciprocal PfGexp18_MinStd PfGexp18_MaxDilution PfGexp18_MaxStd PfGexp18_MinDilution PvEBP_Adjloglog_Dilution Pv-fam-a_Adjloglog_Dilution PvMSP5_Adjloglog_Dilution PvMSP1-19_Adjloglog_Dilution PvMSP8_Adjloglog_Dilution PvPTEX150_Adjloglog_Dilution PvCSS_Adjloglog_Dilution PvRBP2b_Adjloglog_Dilution
ABC-0001 13(1,B1) B1 Unknown13 plate1 601 6.398595 8.631057 0.02 -0.255195 1.721846 14.73796 0.0020262 1.430762 0.0017050 346.0 5.846439 9.847314 0.02 -0.5988432 5.710997 10.13687 5.39e-05 2.526623 1.95e-05 858.0 6.754604 9.278139 0.02 -0.1812443 -7.423291 13.38976 5.53e-05 0.750427 0.0005129 320.0 5.768321 7.38399 0.02 -0.3931855 2.262344 9.049039 7.59e-05 2.686889 0.0019577 pass 389.0 0.0000834 11989.153 159 3.2e-05 17367 0.02 392 0.0000852 11734.987 174.5 3.2e-05 12754 0.02 502 1.95e-05 51200 3558.5 3.2e-05 26809.5 0.02 387.0 0.0000966 10352.514 149 3.2e-05 13445 0.02 831.5 0.0000400 25018.250 713 3.2e-05 23660.5 0.02 438.0 0.0007845 1274.6183 37 3.2e-05 6152 0.02 556.0 0.0007194 1390.0619 37 3.2e-05 7636 0.02 303.0 0.0000233 43006.509 387 3.2e-05 23226 0.02 363 0.0004380 2283.2281 69 3.2e-05 2751.5 0.02 359.5 0.0011172 895.0603 37 3.2e-05 3007 0.02 467 0.0050186 199.25926 17 3.2e-05 1459 0.02 384.0 0.0061629 162.26245 12 3.2e-05 988 0.02 1113 0.0052569 190.22706 20 3.2e-05 2892 0.02 0.0000258 0.0000923 0.0000800 0.0000762 0.0000195 0.0001358 0.0002014 1.95e-05
ABC-0002 14(1,B2) B2 Unknown14 plate1 344 5.840642 8.631057 0.02 -0.255195 1.721846 14.73796 0.0020262 1.430762 0.0008863 228.5 5.431536 9.847314 0.02 -0.5988432 5.710997 10.13687 5.39e-05 2.526623 1.95e-05 384.0 5.950643 9.278139 0.02 -0.1812443 -7.423291 13.38976 5.53e-05 0.750427 0.0001858 112.5 4.722953 7.38399 0.02 -0.3931855 2.262344 9.049039 7.59e-05 2.686889 0.0005509 pass 217.0 0.0000441 22679.984 159 3.2e-05 17367 0.02 242 0.0000476 21021.638 174.5 3.2e-05 12754 0.02 337 1.95e-05 51200 3558.5 3.2e-05 26809.5 0.02 226.0 0.0000518 19298.142 149 3.2e-05 13445 0.02 532.0 0.0000199 50141.217 713 3.2e-05 23660.5 0.02 171.0 0.0002491 4014.0622 37 3.2e-05 6152 0.02 377.0 0.0004554 2196.0002 37 3.2e-05 7636 0.02 483.0 0.0000423 23632.795 387 3.2e-05 23226 0.02 234 0.0002323 4304.3814 69 3.2e-05 2751.5 0.02 229.0 0.0006105 1638.0163 37 3.2e-05 3007 0.02 319 0.0031701 315.45144 17 3.2e-05 1459 0.02 256.0 0.0038047 262.83255 12 3.2e-05 988 0.02 634 0.0026246 381.01243 20 3.2e-05 2892 0.02 0.0000195 0.0000384 0.0000281 0.0000566 0.0000195 0.0000865 0.0000687 1.95e-05
ABC-0003 15(1,B3) B3 Unknown15 plate1 716 6.573680 8.631057 0.02 -0.255195 1.721846 14.73796 0.0020262 1.430762 0.0020814 584.0 6.369901 9.847314 0.02 -0.5988432 5.710997 10.13687 5.39e-05 2.526623 4.43e-05 4397.0 8.388678 9.278139 0.02 -0.1812443 -7.423291 13.38976 5.53e-05 0.750427 0.0049878 271.0 5.602119 7.38399 0.02 -0.3931855 2.262344 9.049039 7.59e-05 2.686889 0.0015958 pass 634.0 0.0001442 6936.335 159 3.2e-05 17367 0.02 663 0.0001601 6246.280 174.5 3.2e-05 12754 0.02 656 1.95e-05 51200 3558.5 3.2e-05 26809.5 0.02 673.5 0.0001845 5420.041 149 3.2e-05 13445 0.02 1390.5 0.0000777 12863.776 713 3.2e-05 23660.5 0.02 671.0 0.0013071 765.0369 37 3.2e-05 6152 0.02 731.5 0.0009975 1002.5234 37 3.2e-05 7636 0.02 519.0 0.0000463 21621.543 387 3.2e-05 23226 0.02 596 0.0009122 1096.3018 69 3.2e-05 2751.5 0.02 569.5 0.0020438 489.2749 37 3.2e-05 3007 0.02 913 0.0112317 89.03411 17 3.2e-05 1459 0.02 637.5 0.0114129 87.62002 12 3.2e-05 988 0.02 2061 0.0120404 83.05405 20 3.2e-05 2892 0.02 0.0000784 0.0001591 0.0001564 0.0000969 0.0000195 0.0001867 0.0003170 3.09e-05
ABC-0004 16(1,B4) B4 Unknown16 plate1 357 5.877736 8.631057 0.02 -0.255195 1.721846 14.73796 0.0020262 1.430762 0.0009267 235.0 5.459586 9.847314 0.02 -0.5988432 5.710997 10.13687 5.39e-05 2.526623 1.95e-05 437.5 6.081077 9.278139 0.02 -0.1812443 -7.423291 13.38976 5.53e-05 0.750427 0.0002184 143.5 4.966335 7.38399 0.02 -0.3931855 2.262344 9.049039 7.59e-05 2.686889 0.0007403 pass 238.0 0.0000487 20520.215 159 3.2e-05 17367 0.02 283 0.0000575 17378.322 174.5 3.2e-05 12754 0.02 318 1.95e-05 51200 3558.5 3.2e-05 26809.5 0.02 269.0 0.0000634 15768.912 149 3.2e-05 13445 0.02 582.0 0.0000233 42963.675 713 3.2e-05 23660.5 0.02 226.0 0.0003518 2842.7736 37 3.2e-05 6152 0.02 419.0 0.0005154 1940.4208 37 3.2e-05 7636 0.02 205.5 0.0000195 51200.000 387 3.2e-05 23226 0.02 266 0.0002796 3575.9145 69 3.2e-05 2751.5 0.02 265.0 0.0007440 1344.0629 37 3.2e-05 3007 0.02 322 0.0032063 311.89007 17 3.2e-05 1459 0.02 261.5 0.0039019 256.28686 12 3.2e-05 988 0.02 854 0.0037705 265.21947 20 3.2e-05 2892 0.02 0.0000195 0.0000484 0.0000408 0.0000542 0.0000195 0.0000978 0.0000959 1.95e-05
ABC-0005 17(1,B5) B5 Unknown17 plate1 1320 7.185387 8.631057 0.02 -0.255195 1.721846 14.73796 0.0020262 1.430762 0.0041184 746.0 6.614726 9.847314 0.02 -0.5988432 5.710997 10.13687 5.39e-05 2.526623 6.74e-05 1620.0 7.390181 9.278139 0.02 -0.1812443 -7.423291 13.38976 5.53e-05 0.750427 0.0011922 778.0 6.656727 7.38399 0.02 -0.3931855 2.262344 9.049039 7.59e-05 2.686889 0.0063384 pass 746.0 0.0001737 5757.718 159 3.2e-05 17367 0.02 892 0.0002294 4360.066 174.5 3.2e-05 12754 0.02 1352 1.95e-05 51200 3558.5 3.2e-05 26809.5 0.02 918.5 0.0002673 3740.619 149 3.2e-05 13445 0.02 1768.0 0.0001038 9632.643 713 3.2e-05 23660.5 0.02 666.5 0.0012967 771.2116 37 3.2e-05 6152 0.02 1220.5 0.0018551 539.0675 37 3.2e-05 7636 0.02 760.5 0.0000735 13605.973 387 3.2e-05 23226 0.02 846 0.0015869 630.1508 69 3.2e-05 2751.5 0.02 801.0 0.0031965 312.8449 37 3.2e-05 3007 0.02 1048 0.0132789 75.30767 17 3.2e-05 1459 0.02 852.0 0.0164593 60.75578 12 3.2e-05 988 0.02 2191 0.0131474 76.06085 20 3.2e-05 2892 0.02 0.0001145 0.0001912 0.0002249 0.0001941 0.0000417 0.0003388 0.0003148 5.54e-05
ABC-0006 18(1,B6) B6 Unknown18 plate1 899 6.801283 8.631057 0.02 -0.255195 1.721846 14.73796 0.0020262 1.430762 0.0026892 733.0 6.597146 9.847314 0.02 -0.5988432 5.710997 10.13687 5.39e-05 2.526623 6.55e-05 2702.5 7.901933 9.278139 0.02 -0.1812443 -7.423291 13.38976 5.53e-05 0.750427 0.0024354 1015.0 6.922644 7.38399 0.02 -0.3931855 2.262344 9.049039 7.59e-05 2.686889 0.0094357 pass 677.5 0.0001555 6430.683 159 3.2e-05 17367 0.02 895 0.0002303 4342.230 174.5 3.2e-05 12754 0.02 861 1.95e-05 51200 3558.5 3.2e-05 26809.5 0.02 888.0 0.0002566 3896.375 149 3.2e-05 13445 0.02 1728.0 0.0001010 9898.976 713 3.2e-05 23660.5 0.02 579.0 0.0010959 912.4657 37 3.2e-05 6152 0.02 967.5 0.0013973 715.6797 37 3.2e-05 7636 0.02 4955.0 0.0007581 1319.146 387 3.2e-05 23226 0.02 835 0.0015532 643.8484 69 3.2e-05 2751.5 0.02 788.5 0.0031310 319.3872 37 3.2e-05 3007 0.02 1040 0.0131555 76.01376 17 3.2e-05 1459 0.02 829.0 0.0158912 62.92790 12 3.2e-05 988 0.02 2080 0.0121993 81.97173 20 3.2e-05 2892 0.02 0.0001100 0.0001715 0.0002259 0.0001240 0.0006634 0.0002583 0.0002714 5.36e-05

MFI and RAU only:

results_5stdcurve$mfi_outputs$MFI_RAU %>%
  head() %>% 
  kable()
SampleID Plate Pk8_MFI PkMSP10_MFI PkSERA3Ag2_MFI PkSSP2_MFI Pv-fam-a_MFI PvMSP5_MFI PvMSP1-19_MFI PvEBP_MFI PvRBP2b_MFI PvCSS_MFI PvPTEX150_MFI PvMSP8_MFI PfMSP1-19_MFI PfAMA1_MFI Pfetramp5Ag1_MFI PfHSP40Ag1_MFI PfGexp18_MFI Pk8_Dilution PkMSP10_Dilution PkSERA3Ag2_Dilution PkSSP2_Dilution Pv-fam-a_loglog_Dilution PvMSP5_loglog_Dilution PvMSP1-19_loglog_Dilution PvEBP_loglog_Dilution PvRBP2b_loglog_Dilution PvCSS_loglog_Dilution PvPTEX150_loglog_Dilution PvMSP8_loglog_Dilution PfMSP1-19_loglog_Dilution PfAMA1_loglog_Dilution Pfetramp5Ag1_loglog_Dilution PfHSP40Ag1_loglog_Dilution PfGexp18_loglog_Dilution PvEBP_Adjloglog_Dilution Pv-fam-a_Adjloglog_Dilution PvMSP5_Adjloglog_Dilution PvMSP1-19_Adjloglog_Dilution PvMSP8_Adjloglog_Dilution PvPTEX150_Adjloglog_Dilution PvCSS_Adjloglog_Dilution PvRBP2b_Adjloglog_Dilution
ABC-0001 plate1 601 346.0 858.0 320.0 389.0 392 502 387.0 831.5 438.0 556.0 303.0 363 359.5 467 384.0 1113 0.0017050 1.95e-05 0.0005129 0.0019577 0.0000834 0.0000852 1.95e-05 0.0000966 0.0000400 0.0007845 0.0007194 0.0000233 0.0004380 0.0011172 0.0050186 0.0061629 0.0052569 0.0000258 0.0000923 0.0000800 0.0000762 0.0000195 0.0001358 0.0002014 1.95e-05
ABC-0002 plate1 344 228.5 384.0 112.5 217.0 242 337 226.0 532.0 171.0 377.0 483.0 234 229.0 319 256.0 634 0.0008863 1.95e-05 0.0001858 0.0005509 0.0000441 0.0000476 1.95e-05 0.0000518 0.0000199 0.0002491 0.0004554 0.0000423 0.0002323 0.0006105 0.0031701 0.0038047 0.0026246 0.0000195 0.0000384 0.0000281 0.0000566 0.0000195 0.0000865 0.0000687 1.95e-05
ABC-0003 plate1 716 584.0 4397.0 271.0 634.0 663 656 673.5 1390.5 671.0 731.5 519.0 596 569.5 913 637.5 2061 0.0020814 4.43e-05 0.0049878 0.0015958 0.0001442 0.0001601 1.95e-05 0.0001845 0.0000777 0.0013071 0.0009975 0.0000463 0.0009122 0.0020438 0.0112317 0.0114129 0.0120404 0.0000784 0.0001591 0.0001564 0.0000969 0.0000195 0.0001867 0.0003170 3.09e-05
ABC-0004 plate1 357 235.0 437.5 143.5 238.0 283 318 269.0 582.0 226.0 419.0 205.5 266 265.0 322 261.5 854 0.0009267 1.95e-05 0.0002184 0.0007403 0.0000487 0.0000575 1.95e-05 0.0000634 0.0000233 0.0003518 0.0005154 0.0000195 0.0002796 0.0007440 0.0032063 0.0039019 0.0037705 0.0000195 0.0000484 0.0000408 0.0000542 0.0000195 0.0000978 0.0000959 1.95e-05
ABC-0005 plate1 1320 746.0 1620.0 778.0 746.0 892 1352 918.5 1768.0 666.5 1220.5 760.5 846 801.0 1048 852.0 2191 0.0041184 6.74e-05 0.0011922 0.0063384 0.0001737 0.0002294 1.95e-05 0.0002673 0.0001038 0.0012967 0.0018551 0.0000735 0.0015869 0.0031965 0.0132789 0.0164593 0.0131474 0.0001145 0.0001912 0.0002249 0.0001941 0.0000417 0.0003388 0.0003148 5.54e-05
ABC-0006 plate1 899 733.0 2702.5 1015.0 677.5 895 861 888.0 1728.0 579.0 967.5 4955.0 835 788.5 1040 829.0 2080 0.0026892 6.55e-05 0.0024354 0.0094357 0.0001555 0.0002303 1.95e-05 0.0002566 0.0001010 0.0010959 0.0013973 0.0007581 0.0015532 0.0031310 0.0131555 0.0158912 0.0121993 0.0001100 0.0001715 0.0002259 0.0001240 0.0006634 0.0002583 0.0002714 5.36e-05

MFI and RAU long table:

results_5stdcurve$mfi_outputs$MFI_RAU_long %>%
  head() %>% 
  kable()
SampleID Plate Antigens Species MFI RAU RAU_Method
ABC-0001 plate1 Pk8 Pk 601 0.0017050 loglog
ABC-0001 plate1 PkMSP10 Pk 346 0.0000195 loglog
ABC-0001 plate1 PkSERA3Ag2 Pk 858 0.0005129 loglog
ABC-0001 plate1 PkSSP2 Pk 320 0.0019577 loglog
ABC-0001 plate1 Pv-fam-a Pv 389 0.0000834 loglog
ABC-0001 plate1 Pv-fam-a Pv 389 0.0000923 Adj_loglog

10-Point Standard Curve

These steps are very similar to the 5-point standard curve, except where indicated.

Step 1: Load your data! 

your_raw_data_10std <- c(
  system.file("extdata", "example_MAGPIX_pk_10std_plate1.csv", package = "SeroTrackR"),
  system.file("extdata", "example_MAGPIX_pk_10std_plate2.csv", package = "SeroTrackR")
)
your_plate_layout_10std <- system.file("extdata", "example_platelayout_pk_10std.xlsx", package = "SeroTrackR")

Step 2: Read your data and process MFI to RAU 

results_10stdcurve <- runPlasmoPipeline(
  raw_data = your_raw_data_10std,
  platform = "magpix",
  plate_layout = your_plate_layout_10std,
  panel = "panel1",
  std_point = 10, ################################### here make sure you write 10! 
  experiment_name = "10-point standard curve"
)
#> PASS: File example_magpix_pk_10std_plate1.csv successfully validated.
#> PASS: File example_magpix_pk_10std_plate2.csv successfully validated.
#> Plate layouts correctly identified!
#> QC Processes completed.
#> QC Plotting completed.
#> MFI to RAU conversion completed.
#> Pv classification completed.
Standard Curve Plot 
results_10stdcurve$std_curve

Bead Counts QC Plot 
results_10stdcurve$bead_counts

Blanks QC Ploat 
results_10stdcurve$blanks

MFI to RAU Tables

All results:

results_10stdcurve$mfi_outputs$All_Results %>%
  head() %>% 
  kable()
SampleID Location Location.2 Sample Plate Pk8_MFI Pk8_log_mfi Pk8_max_s1 Pk8_max_dil Pk8_slope Pk8_low_asym Pk8_upp_asym Pk8_ed50 Pk8_asym_par Pk8_Dilution PkMSP10_MFI PkMSP10_log_mfi PkMSP10_max_s1 PkMSP10_max_dil PkMSP10_slope PkMSP10_low_asym PkMSP10_upp_asym PkMSP10_ed50 PkMSP10_asym_par PkMSP10_Dilution PkSERA3Ag2_MFI PkSERA3Ag2_log_mfi PkSERA3Ag2_max_s1 PkSERA3Ag2_max_dil PkSERA3Ag2_slope PkSERA3Ag2_low_asym PkSERA3Ag2_upp_asym PkSERA3Ag2_ed50 PkSERA3Ag2_asym_par PkSERA3Ag2_Dilution PkSSP2_MFI PkSSP2_log_mfi PkSSP2_max_s1 PkSSP2_max_dil PkSSP2_slope PkSSP2_low_asym PkSSP2_upp_asym PkSSP2_ed50 PkSSP2_asym_par PkSSP2_Dilution QC_total Pv-fam-a_MFI Pv-fam-a_loglog_Dilution Pv-fam-a_DilutionReciprocal Pv-fam-a_MinStd Pv-fam-a_MaxDilution Pv-fam-a_MaxStd Pv-fam-a_MinDilution PvMSP5_MFI PvMSP5_loglog_Dilution PvMSP5_DilutionReciprocal PvMSP5_MinStd PvMSP5_MaxDilution PvMSP5_MaxStd PvMSP5_MinDilution PvMSP1-19_MFI PvMSP1-19_loglog_Dilution PvMSP1-19_DilutionReciprocal PvMSP1-19_MinStd PvMSP1-19_MaxDilution PvMSP1-19_MaxStd PvMSP1-19_MinDilution PvEBP_MFI PvEBP_loglog_Dilution PvEBP_DilutionReciprocal PvEBP_MinStd PvEBP_MaxDilution PvEBP_MaxStd PvEBP_MinDilution PvRBP2b_MFI PvRBP2b_loglog_Dilution PvRBP2b_DilutionReciprocal PvRBP2b_MinStd PvRBP2b_MaxDilution PvRBP2b_MaxStd PvRBP2b_MinDilution PvCSS_MFI PvCSS_loglog_Dilution PvCSS_DilutionReciprocal PvCSS_MinStd PvCSS_MaxDilution PvCSS_MaxStd PvCSS_MinDilution PvPTEX150_MFI PvPTEX150_loglog_Dilution PvPTEX150_DilutionReciprocal PvPTEX150_MinStd PvPTEX150_MaxDilution PvPTEX150_MaxStd PvPTEX150_MinDilution PvMSP8_MFI PvMSP8_loglog_Dilution PvMSP8_DilutionReciprocal PvMSP8_MinStd PvMSP8_MaxDilution PvMSP8_MaxStd PvMSP8_MinDilution PfMSP1-19_MFI PfMSP1-19_loglog_Dilution PfMSP1-19_DilutionReciprocal PfMSP1-19_MinStd PfMSP1-19_MaxDilution PfMSP1-19_MaxStd PfMSP1-19_MinDilution PfAMA1_MFI PfAMA1_loglog_Dilution PfAMA1_DilutionReciprocal PfAMA1_MinStd PfAMA1_MaxDilution PfAMA1_MaxStd PfAMA1_MinDilution Pfetramp5Ag1_MFI Pfetramp5Ag1_loglog_Dilution Pfetramp5Ag1_DilutionReciprocal Pfetramp5Ag1_MinStd Pfetramp5Ag1_MaxDilution Pfetramp5Ag1_MaxStd Pfetramp5Ag1_MinDilution PfHSP40Ag1_MFI PfHSP40Ag1_loglog_Dilution PfHSP40Ag1_DilutionReciprocal PfHSP40Ag1_MinStd PfHSP40Ag1_MaxDilution PfHSP40Ag1_MaxStd PfHSP40Ag1_MinDilution PfGexp18_MFI PfGexp18_loglog_Dilution PfGexp18_DilutionReciprocal PfGexp18_MinStd PfGexp18_MaxDilution PfGexp18_MaxStd PfGexp18_MinDilution PvEBP_Adjloglog_Dilution Pv-fam-a_Adjloglog_Dilution PvMSP5_Adjloglog_Dilution PvMSP1-19_Adjloglog_Dilution PvMSP8_Adjloglog_Dilution PvPTEX150_Adjloglog_Dilution PvCSS_Adjloglog_Dilution PvRBP2b_Adjloglog_Dilution
ABC-0001 25(1,C1) C1 Unknown25 plate1 1953.0 7.577122 10.11523 0.02 -4.204756 -10.30704 8.564423 0.0006965 0.0135688 0.0002728 1095.0 6.998510 9.938372 0.02 -3.189255 2.67481 8.666433 0.0005417 0.0673257 0.0001188 5761.0 8.658866 8.724207 0.02 -3.933689 0.0330379 6.955764 0.0007694 0.0511217 0.0000195 901.5 6.804060 9.752665 0.02 -3.125431 0.1110772 8.270073 0.0007182 0.0458122 0.0001809 pass 1020 0.0009250 1081.0739 44 3.91e-05 13024 0.02 1987.0 0.0006427 1555.8711 161 3.91e-05 24023.5 0.02 5070 0.0019239 519.7885 121.5 3.91e-05 23687 0.02 3140 0.0011043 905.5270 116 3.91e-05 17664 0.02 15170.0 0.0200000 50.0000 86 3.91e-05 9648 0.02 672.0 0.0007168 1395.065 29 3.91e-05 13146.5 0.02 1350 0.0011266 887.5992 52.5 3.91e-05 14354 0.02 1751.0 0.0004915 2034.5996 167 3.91e-05 24512 0.02 1221 0.0200000 50.0000 26 3.91e-05 792.5 0.02 873.5 0.0022286 448.7084 42 3.91e-05 2658 0.02 1058.0 0.0200000 50.0000 23.5 3.91e-05 1009 0.02 863.0 0.0200000 50.00000 15 3.91e-05 438 0.02 2303.0 0.0014797 675.8095 211 3.91e-05 9475 0.02 0.0005117 0.0010659 0.0005896 0.0165594 0.0004472 0.0002156 0.0001776 0.0181453
ABC-0002 26(1,C2) C2 Unknown26 plate1 492.5 6.199495 10.11523 0.02 -4.204756 -10.30704 8.564423 0.0006965 0.0135688 0.0000666 296.5 5.692047 9.938372 0.02 -3.189255 2.67481 8.666433 0.0005417 0.0673257 0.0000222 4583.0 8.430109 8.724207 0.02 -3.933689 0.0330379 6.955764 0.0007694 0.0511217 0.0000195 214.5 5.368310 9.752665 0.02 -3.125431 0.1110772 8.270073 0.0007182 0.0458122 0.0000334 pass 329 0.0003249 3077.4498 44 3.91e-05 13024 0.02 369.5 0.0001130 8852.8029 161 3.91e-05 24023.5 0.02 521 0.0001926 5191.2030 121.5 3.91e-05 23687 0.02 346 0.0001220 8195.5655 116 3.91e-05 17664 0.02 778.0 0.0004303 2324.0862 86 3.91e-05 9648 0.02 264.5 0.0003275 3053.058 29 3.91e-05 13146.5 0.02 500 0.0004606 2171.2319 52.5 3.91e-05 14354 0.02 324.0 0.0000843 11861.3051 167 3.91e-05 24512 0.02 364 0.0032324 309.3656 26 3.91e-05 792.5 0.02 366.0 0.0006612 1512.4968 42 3.91e-05 2658 0.02 462.5 0.0037562 266.2252 23.5 3.91e-05 1009 0.02 368.5 0.0137142 72.91694 15 3.91e-05 438 0.02 1003.5 0.0003593 2783.1779 211 3.91e-05 9475 0.02 0.0000385 0.0003910 0.0000999 0.0019141 0.0000467 0.0000873 0.0000815 0.0002659
ABC-0003 27(1,C3) C3 Unknown27 plate1 136.5 4.916325 10.11523 0.02 -4.204756 -10.30704 8.564423 0.0006965 0.0135688 0.0000195 36.0 3.583519 9.938372 0.02 -3.189255 2.67481 8.666433 0.0005417 0.0673257 0.0000195 465.0 6.142037 8.724207 0.02 -3.933689 0.0330379 6.955764 0.0007694 0.0511217 0.0004228 63.0 4.143135 9.752665 0.02 -3.125431 0.1110772 8.270073 0.0007182 0.0458122 0.0000195 pass 64 0.0000636 15720.7543 44 3.91e-05 13024 0.02 50.0 0.0000195 51200.0000 161 3.91e-05 24023.5 0.02 113 0.0000375 26646.4247 121.5 3.91e-05 23687 0.02 45 0.0000195 51200.0000 116 3.91e-05 17664 0.02 726.0 0.0003985 2509.3247 86 3.91e-05 9648 0.02 101.5 0.0001440 6945.366 29 3.91e-05 13146.5 0.02 1124 0.0009516 1050.9046 52.5 3.91e-05 14354 0.02 52.0 0.0000195 51200.0000 167 3.91e-05 24512 0.02 66 0.0002067 4838.7924 26 3.91e-05 792.5 0.02 75.0 0.0000871 11484.8827 42 3.91e-05 2658 0.02 64.0 0.0001930 5180.1406 23.5 3.91e-05 1009 0.02 60.0 0.0003634 2751.99662 15 3.91e-05 438 0.02 137.0 0.0000195 51200.0000 211 3.91e-05 9475 0.02 0.0000195 0.0000557 0.0000195 0.0006034 0.0000195 0.0001827 0.0000299 0.0002456
ABC-0004 28(1,C4) C4 Unknown28 plate1 464.0 6.139885 10.11523 0.02 -4.204756 -10.30704 8.564423 0.0006965 0.0135688 0.0000625 688.5 6.534515 9.938372 0.02 -3.189255 2.67481 8.666433 0.0005417 0.0673257 0.0000699 204.0 5.318120 8.724207 0.02 -3.933689 0.0330379 6.955764 0.0007694 0.0511217 0.0002013 6687.0 8.807921 9.752665 0.02 -3.125431 0.1110772 8.270073 0.0007182 0.0458122 0.0000195 pass 777 0.0007167 1395.2938 44 3.91e-05 13024 0.02 4357.0 0.0015093 662.5724 161 3.91e-05 24023.5 0.02 273 0.0001013 9872.2137 121.5 3.91e-05 23687 0.02 998 0.0003335 2998.8421 116 3.91e-05 17664 0.02 2673.0 0.0019523 512.2274 86 3.91e-05 9648 0.02 213.0 0.0002731 3661.742 29 3.91e-05 13146.5 0.02 425 0.0003985 2509.2529 52.5 3.91e-05 14354 0.02 3718.0 0.0011290 885.7238 167 3.91e-05 24512 0.02 251 0.0016733 597.6085 26 3.91e-05 792.5 0.02 876.0 0.0022385 446.7223 42 3.91e-05 2658 0.02 275.0 0.0015646 639.1509 23.5 3.91e-05 1009 0.02 227.0 0.0045270 220.89449 15 3.91e-05 438 0.02 499.0 0.0001171 8538.4610 211 3.91e-05 9475 0.02 0.0001404 0.0008412 0.0013207 0.0011681 0.0010458 0.0000750 0.0000678 0.0011763
ABC-0005 29(1,C5) C5 Unknown29 plate1 2159.0 7.677400 10.11523 0.02 -4.204756 -10.30704 8.564423 0.0006965 0.0135688 0.0003016 1047.5 6.954162 9.938372 0.02 -3.189255 2.67481 8.666433 0.0005417 0.0673257 0.0001132 1563.0 7.354362 8.724207 0.02 -3.933689 0.0330379 6.955764 0.0007694 0.0511217 0.0000195 1002.5 6.910252 9.752665 0.02 -3.125431 0.1110772 8.270073 0.0007182 0.0458122 0.0002022 pass 1434 0.0012831 779.3828 44 3.91e-05 13024 0.02 2218.0 0.0007210 1387.0041 161 3.91e-05 24023.5 0.02 2318 0.0008246 1212.6887 121.5 3.91e-05 23687 0.02 3161 0.0011129 898.5615 116 3.91e-05 17664 0.02 14703.5 0.0200000 50.0000 86 3.91e-05 9648 0.02 1764.5 0.0016960 589.621 29 3.91e-05 13146.5 0.02 1730 0.0014235 702.4696 52.5 3.91e-05 14354 0.02 3042.5 0.0008983 1113.1736 167 3.91e-05 24512 0.02 903 0.0200000 50.0000 26 3.91e-05 792.5 0.02 696.5 0.0015869 630.1708 42 3.91e-05 2658 0.02 1259.0 0.0200000 50.0000 23.5 3.91e-05 1009 0.02 765.0 0.0200000 50.00000 15 3.91e-05 438 0.02 1867.0 0.0010243 976.2313 211 3.91e-05 9475 0.02 0.0005156 0.0014398 0.0006586 0.0080539 0.0008397 0.0002702 0.0004059 0.0180255
ABC-0006 30(1,C6) C6 Unknown30 plate1 313.5 5.747799 10.11523 0.02 -4.204756 -10.30704 8.564423 0.0006965 0.0135688 0.0000410 317.0 5.758902 9.938372 0.02 -3.189255 2.67481 8.666433 0.0005417 0.0673257 0.0000246 4176.5 8.337229 8.724207 0.02 -3.933689 0.0330379 6.955764 0.0007694 0.0511217 0.0000195 157.0 5.056246 9.752665 0.02 -3.125431 0.1110772 8.270073 0.0007182 0.0458122 0.0000218 pass 173 0.0001779 5620.5138 44 3.91e-05 13024 0.02 244.5 0.0000706 14166.0632 161 3.91e-05 24023.5 0.02 1211 0.0004337 2305.8063 121.5 3.91e-05 23687 0.02 717 0.0002429 4117.2900 116 3.91e-05 17664 0.02 1808.0 0.0011610 861.3537 86 3.91e-05 9648 0.02 164.0 0.0002188 4570.580 29 3.91e-05 13146.5 0.02 242 0.0002391 4182.3555 52.5 3.91e-05 14354 0.02 640.0 0.0001721 5809.2375 167 3.91e-05 24512 0.02 292 0.0021690 461.0460 26 3.91e-05 792.5 0.02 243.0 0.0003930 2544.3740 42 3.91e-05 2658 0.02 243.0 0.0012934 773.1434 23.5 3.91e-05 1009 0.02 213.5 0.0039745 251.60296 15 3.91e-05 438 0.02 410.0 0.0000862 11599.5225 211 3.91e-05 9475 0.02 0.0000975 0.0002066 0.0000592 0.0039599 0.0001246 0.0000393 0.0000524 0.0007162

MFI and RAU only:

results_10stdcurve$mfi_outputs$MFI_RAU %>%
  head() %>% 
  kable()
SampleID Plate Pk8_MFI PkMSP10_MFI PkSERA3Ag2_MFI PkSSP2_MFI Pv-fam-a_MFI PvMSP5_MFI PvMSP1-19_MFI PvEBP_MFI PvRBP2b_MFI PvCSS_MFI PvPTEX150_MFI PvMSP8_MFI PfMSP1-19_MFI PfAMA1_MFI Pfetramp5Ag1_MFI PfHSP40Ag1_MFI PfGexp18_MFI Pk8_Dilution PkMSP10_Dilution PkSERA3Ag2_Dilution PkSSP2_Dilution Pv-fam-a_loglog_Dilution PvMSP5_loglog_Dilution PvMSP1-19_loglog_Dilution PvEBP_loglog_Dilution PvRBP2b_loglog_Dilution PvCSS_loglog_Dilution PvPTEX150_loglog_Dilution PvMSP8_loglog_Dilution PfMSP1-19_loglog_Dilution PfAMA1_loglog_Dilution Pfetramp5Ag1_loglog_Dilution PfHSP40Ag1_loglog_Dilution PfGexp18_loglog_Dilution PvEBP_Adjloglog_Dilution Pv-fam-a_Adjloglog_Dilution PvMSP5_Adjloglog_Dilution PvMSP1-19_Adjloglog_Dilution PvMSP8_Adjloglog_Dilution PvPTEX150_Adjloglog_Dilution PvCSS_Adjloglog_Dilution PvRBP2b_Adjloglog_Dilution
ABC-0001 plate1 1953.0 1095.0 5761.0 901.5 1020 1987.0 5070 3140 15170.0 672.0 1350 1751.0 1221 873.5 1058.0 863.0 2303.0 0.0002728 0.0001188 0.0000195 0.0001809 0.0009250 0.0006427 0.0019239 0.0011043 0.0200000 0.0007168 0.0011266 0.0004915 0.0200000 0.0022286 0.0200000 0.0200000 0.0014797 0.0005117 0.0010659 0.0005896 0.0165594 0.0004472 0.0002156 0.0001776 0.0181453
ABC-0002 plate1 492.5 296.5 4583.0 214.5 329 369.5 521 346 778.0 264.5 500 324.0 364 366.0 462.5 368.5 1003.5 0.0000666 0.0000222 0.0000195 0.0000334 0.0003249 0.0001130 0.0001926 0.0001220 0.0004303 0.0003275 0.0004606 0.0000843 0.0032324 0.0006612 0.0037562 0.0137142 0.0003593 0.0000385 0.0003910 0.0000999 0.0019141 0.0000467 0.0000873 0.0000815 0.0002659
ABC-0003 plate1 136.5 36.0 465.0 63.0 64 50.0 113 45 726.0 101.5 1124 52.0 66 75.0 64.0 60.0 137.0 0.0000195 0.0000195 0.0004228 0.0000195 0.0000636 0.0000195 0.0000375 0.0000195 0.0003985 0.0001440 0.0009516 0.0000195 0.0002067 0.0000871 0.0001930 0.0003634 0.0000195 0.0000195 0.0000557 0.0000195 0.0006034 0.0000195 0.0001827 0.0000299 0.0002456
ABC-0004 plate1 464.0 688.5 204.0 6687.0 777 4357.0 273 998 2673.0 213.0 425 3718.0 251 876.0 275.0 227.0 499.0 0.0000625 0.0000699 0.0002013 0.0000195 0.0007167 0.0015093 0.0001013 0.0003335 0.0019523 0.0002731 0.0003985 0.0011290 0.0016733 0.0022385 0.0015646 0.0045270 0.0001171 0.0001404 0.0008412 0.0013207 0.0011681 0.0010458 0.0000750 0.0000678 0.0011763
ABC-0005 plate1 2159.0 1047.5 1563.0 1002.5 1434 2218.0 2318 3161 14703.5 1764.5 1730 3042.5 903 696.5 1259.0 765.0 1867.0 0.0003016 0.0001132 0.0000195 0.0002022 0.0012831 0.0007210 0.0008246 0.0011129 0.0200000 0.0016960 0.0014235 0.0008983 0.0200000 0.0015869 0.0200000 0.0200000 0.0010243 0.0005156 0.0014398 0.0006586 0.0080539 0.0008397 0.0002702 0.0004059 0.0180255
ABC-0006 plate1 313.5 317.0 4176.5 157.0 173 244.5 1211 717 1808.0 164.0 242 640.0 292 243.0 243.0 213.5 410.0 0.0000410 0.0000246 0.0000195 0.0000218 0.0001779 0.0000706 0.0004337 0.0002429 0.0011610 0.0002188 0.0002391 0.0001721 0.0021690 0.0003930 0.0012934 0.0039745 0.0000862 0.0000975 0.0002066 0.0000592 0.0039599 0.0001246 0.0000393 0.0000524 0.0007162

MFI and RAU long table:

results_10stdcurve$mfi_outputs$MFI_RAU_long %>%
  head() %>% 
  kable()
SampleID Plate Antigens Species MFI RAU RAU_Method
ABC-0001 plate1 Pk8 Pk 1953.0 0.0002728 loglog
ABC-0001 plate1 PkMSP10 Pk 1095.0 0.0001188 loglog
ABC-0001 plate1 PkSERA3Ag2 Pk 5761.0 0.0000195 loglog
ABC-0001 plate1 PkSSP2 Pk 901.5 0.0001809 loglog
ABC-0001 plate1 Pv-fam-a Pv 1020.0 0.0009250 loglog
ABC-0001 plate1 Pv-fam-a Pv 1020.0 0.0010659 Adj_loglog