Pk/Pv/Pf Serology Tutorial

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

Visualisation of the Pk/Pv/Pf Pipeline

library(SeroTrackR)
library(tidyverse)

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 -0.2551955 1.721849 14.73794 0.0020262 1.430761 0.0017050 346.0 5.846439 9.847314 0.02 -0.5987251 5.705375 10.1375 5.5e-05 2.496542 1.95e-05 858.0 6.754604 9.278139 0.02 -0.1780712 -7.81022 13.47082 4.95e-05 0.7487513 0.0005128 320.0 5.768321 7.38399 0.02 -0.3932893 2.263201 9.048118 7.59e-05 2.688472 0.0019576 pass 389.0 0.0000834 11989.156 159 3.2e-05 17367 0.02 392 0.0000852 11732.800 174.5 3.2e-05 12754 0.02 502 1.95e-05 51200 3558.5 3.2e-05 26809.5 0.02 387.0 0.0000966 10352.513 149 3.2e-05 13445 0.02 831.5 0.0000400 25019.425 713 3.2e-05 23660.5 0.02 438.0 0.0007845 1274.6183 37 3.2e-05 6152 0.02 556.0 0.0007196 1389.6781 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 -0.2551955 1.721849 14.73794 0.0020262 1.430761 0.0008863 228.5 5.431536 9.847314 0.02 -0.5987251 5.705375 10.1375 5.5e-05 2.496542 1.95e-05 384.0 5.950643 9.278139 0.02 -0.1780712 -7.81022 13.47082 4.95e-05 0.7487513 0.0001857 112.5 4.722953 7.38399 0.02 -0.3932893 2.263201 9.048118 7.59e-05 2.688472 0.0005510 pass 217.0 0.0000441 22679.984 159 3.2e-05 17367 0.02 242 0.0000475 21051.010 174.5 3.2e-05 12754 0.02 337 1.95e-05 51200 3558.5 3.2e-05 26809.5 0.02 226.0 0.0000518 19298.141 149 3.2e-05 13445 0.02 532.0 0.0000200 50124.782 713 3.2e-05 23660.5 0.02 171.0 0.0002491 4014.0622 37 3.2e-05 6152 0.02 377.0 0.0004553 2196.2460 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 -0.2551955 1.721849 14.73794 0.0020262 1.430761 0.0020814 584.0 6.369901 9.847314 0.02 -0.5987251 5.705375 10.1375 5.5e-05 2.496542 4.43e-05 4397.0 8.388678 9.278139 0.02 -0.1780712 -7.81022 13.47082 4.95e-05 0.7487513 0.0049920 271.0 5.602119 7.38399 0.02 -0.3932893 2.263201 9.048118 7.59e-05 2.688472 0.0015957 pass 634.0 0.0001442 6936.337 159 3.2e-05 17367 0.02 663 0.0001605 6232.396 174.5 3.2e-05 12754 0.02 656 1.95e-05 51200 3558.5 3.2e-05 26809.5 0.02 673.5 0.0001845 5420.040 149 3.2e-05 13445 0.02 1390.5 0.0000777 12864.423 713 3.2e-05 23660.5 0.02 671.0 0.0013071 765.0369 37 3.2e-05 6152 0.02 731.5 0.0009980 1001.9749 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 -0.2551955 1.721849 14.73794 0.0020262 1.430761 0.0009267 235.0 5.459586 9.847314 0.02 -0.5987251 5.705375 10.1375 5.5e-05 2.496542 1.95e-05 437.5 6.081077 9.278139 0.02 -0.1780712 -7.81022 13.47082 4.95e-05 0.7487513 0.0002183 143.5 4.966335 7.38399 0.02 -0.3932893 2.263201 9.048118 7.59e-05 2.688472 0.0007404 pass 238.0 0.0000487 20520.216 159 3.2e-05 17367 0.02 283 0.0000575 17395.576 174.5 3.2e-05 12754 0.02 318 1.95e-05 51200 3558.5 3.2e-05 26809.5 0.02 269.0 0.0000634 15768.911 149 3.2e-05 13445 0.02 582.0 0.0000233 42955.584 713 3.2e-05 23660.5 0.02 226.0 0.0003518 2842.7736 37 3.2e-05 6152 0.02 419.0 0.0005153 1940.4374 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 -0.2551955 1.721849 14.73794 0.0020262 1.430761 0.0041184 746.0 6.614726 9.847314 0.02 -0.5987251 5.705375 10.1375 5.5e-05 2.496542 6.73e-05 1620.0 7.390181 9.278139 0.02 -0.1780712 -7.81022 13.47082 4.95e-05 0.7487513 0.0011927 778.0 6.656727 7.38399 0.02 -0.3932893 2.263201 9.048118 7.59e-05 2.688472 0.0063379 pass 746.0 0.0001737 5757.719 159 3.2e-05 17367 0.02 892 0.0002301 4346.826 174.5 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 9632.812 713 3.2e-05 23660.5 0.02 666.5 0.0012967 771.2116 37 3.2e-05 6152 0.02 1220.5 0.0018568 538.5466 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 -0.2551955 1.721849 14.73794 0.0020262 1.430761 0.0026892 733.0 6.597146 9.847314 0.02 -0.5987251 5.705375 10.1375 5.5e-05 2.496542 6.55e-05 2702.5 7.901933 9.278139 0.02 -0.1780712 -7.81022 13.47082 4.95e-05 0.7487513 0.0024374 1015.0 6.922644 7.38399 0.02 -0.3932893 2.263201 9.048118 7.59e-05 2.688472 0.0094351 pass 677.5 0.0001555 6430.684 159 3.2e-05 17367 0.02 895 0.0002310 4329.014 174.5 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 9899.182 713 3.2e-05 23660.5 0.02 579.0 0.0010959 912.4657 37 3.2e-05 6152 0.02 967.5 0.0013984 715.1097 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 0.0005128 0.0019576 0.0000834 0.0000852 1.95e-05 0.0000966 0.0000400 0.0007845 0.0007196 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 0.0001857 0.0005510 0.0000441 0.0000475 1.95e-05 0.0000518 0.0000200 0.0002491 0.0004553 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 0.0049920 0.0015957 0.0001442 0.0001605 1.95e-05 0.0001845 0.0000777 0.0013071 0.0009980 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 0.0002183 0.0007404 0.0000487 0.0000575 1.95e-05 0.0000634 0.0000233 0.0003518 0.0005153 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 6.73e-05 0.0011927 0.0063379 0.0001737 0.0002301 1.95e-05 0.0002673 0.0001038 0.0012967 0.0018568 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 0.0024374 0.0094351 0.0001555 0.0002310 1.95e-05 0.0002566 0.0001010 0.0010959 0.0013984 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 0.0005128 loglog
ABC-0001 plate1 PkSSP2 Pk 320 0.0019576 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 -3.502269 -5.329762 8.563494 0.0006473 0.0234765 0.0002677 1095.0 6.998510 9.938372 0.02 -3.189242 2.674833 8.666433 0.0005417 0.0673263 0.0001188 5761.0 8.658866 8.724207 0.02 -3.933692 0.033033 6.955763 0.0007694 0.0511216 0.0000195 901.5 6.804060 9.752665 0.02 -5.271388 -7.016106 8.277811 0.0009076 0.0120942 0.0001852 pass 1020 0.0009249 1081.1509 44 3.91e-05 13024 0.02 1987.0 0.0006430 1555.2489 161 3.91e-05 24023.5 0.02 5070 0.0019237 519.8414 121.5 3.91e-05 23687 0.02 3140 0.0011044 905.4330 116 3.91e-05 17664 0.02 15170.0 0.0200000 50.0000 86 3.91e-05 9648 0.02 672.0 0.0007167 1395.312 29 3.91e-05 13146.5 0.02 1350 0.0011269 887.3778 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 0.0022294 448.5452 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 0.0014803 675.5326 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 -3.502269 -5.329762 8.563494 0.0006473 0.0234765 0.0000670 296.5 5.692047 9.938372 0.02 -3.189242 2.674833 8.666433 0.0005417 0.0673263 0.0000222 4583.0 8.430109 8.724207 0.02 -3.933692 0.033033 6.955763 0.0007694 0.0511216 0.0000195 214.5 5.368310 9.752665 0.02 -5.271388 -7.016106 8.277811 0.0009076 0.0120942 0.0000331 pass 329 0.0003251 3076.3624 44 3.91e-05 13024 0.02 369.5 0.0001129 8855.2357 161 3.91e-05 24023.5 0.02 521 0.0001926 5191.8887 121.5 3.91e-05 23687 0.02 346 0.0001220 8195.1995 116 3.91e-05 17664 0.02 778.0 0.0004303 2324.0862 86 3.91e-05 9648 0.02 264.5 0.0003277 3052.005 29 3.91e-05 13146.5 0.02 500 0.0004604 2171.9440 52.5 3.91e-05 14354 0.02 324.0 0.0000843 11861.3051 167 3.91e-05 24512 0.02 364 0.0032324 309.3678 26 3.91e-05 792.5 0.02 366.0 0.0006608 1513.2624 42 3.91e-05 2658 0.02 462.5 0.0037564 266.2154 23.5 3.91e-05 1009 0.02 368.5 0.0136755 73.12365 15 3.91e-05 438 0.02 1003.5 0.0003596 2780.7962 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 -3.502269 -5.329762 8.563494 0.0006473 0.0234765 0.0000195 36.0 3.583519 9.938372 0.02 -3.189242 2.674833 8.666433 0.0005417 0.0673263 0.0000195 465.0 6.142037 8.724207 0.02 -3.933692 0.033033 6.955763 0.0007694 0.0511216 0.0004228 63.0 4.143135 9.752665 0.02 -5.271388 -7.016106 8.277811 0.0009076 0.0120942 0.0000195 pass 64 0.0000636 15718.6810 44 3.91e-05 13024 0.02 50.0 0.0000195 51200.0000 161 3.91e-05 24023.5 0.02 113 0.0000375 26634.9481 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 0.0001441 6940.063 29 3.91e-05 13146.5 0.02 1124 0.0009517 1050.7398 52.5 3.91e-05 14354 0.02 52.0 0.0000195 51200.0000 167 3.91e-05 24512 0.02 66 0.0002067 4838.8097 26 3.91e-05 792.5 0.02 75.0 0.0000871 11478.5621 42 3.91e-05 2658 0.02 64.0 0.0001926 5193.3446 23.5 3.91e-05 1009 0.02 60.0 0.0003623 2760.01402 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 -3.502269 -5.329762 8.563494 0.0006473 0.0234765 0.0000629 688.5 6.534515 9.938372 0.02 -3.189242 2.674833 8.666433 0.0005417 0.0673263 0.0000699 204.0 5.318120 8.724207 0.02 -3.933692 0.033033 6.955763 0.0007694 0.0511216 0.0002013 6687.0 8.807921 9.752665 0.02 -5.271388 -7.016106 8.277811 0.0009076 0.0120942 0.0000195 pass 777 0.0007167 1395.2532 44 3.91e-05 13024 0.02 4357.0 0.0015092 662.6047 161 3.91e-05 24023.5 0.02 273 0.0001013 9873.6257 121.5 3.91e-05 23687 0.02 998 0.0003335 2998.8618 116 3.91e-05 17664 0.02 2673.0 0.0019523 512.2274 86 3.91e-05 9648 0.02 213.0 0.0002732 3660.034 29 3.91e-05 13146.5 0.02 425 0.0003984 2510.3333 52.5 3.91e-05 14354 0.02 3718.0 0.0011290 885.7238 167 3.91e-05 24512 0.02 251 0.0016733 597.6121 26 3.91e-05 792.5 0.02 876.0 0.0022394 446.5580 42 3.91e-05 2658 0.02 275.0 0.0015668 638.2498 23.5 3.91e-05 1009 0.02 227.0 0.0045507 219.74785 15 3.91e-05 438 0.02 499.0 0.0001171 8536.1964 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 -3.502269 -5.329762 8.563494 0.0006473 0.0234765 0.0002956 1047.5 6.954162 9.938372 0.02 -3.189242 2.674833 8.666433 0.0005417 0.0673263 0.0001132 1563.0 7.354362 8.724207 0.02 -3.933692 0.033033 6.955763 0.0007694 0.0511216 0.0000195 1002.5 6.910252 9.752665 0.02 -5.271388 -7.016106 8.277811 0.0009076 0.0120942 0.0002089 pass 1434 0.0012828 779.5267 44 3.91e-05 13024 0.02 2218.0 0.0007212 1386.4955 161 3.91e-05 24023.5 0.02 2318 0.0008246 1212.7690 121.5 3.91e-05 23687 0.02 3161 0.0011130 898.4671 116 3.91e-05 17664 0.02 14703.5 0.0200000 50.0000 86 3.91e-05 9648 0.02 1764.5 0.0016951 589.928 29 3.91e-05 13146.5 0.02 1730 0.0014241 702.2173 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 0.0015870 630.1390 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 0.0010250 975.6423 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 -3.502269 -5.329762 8.563494 0.0006473 0.0234765 0.0000412 317.0 5.758902 9.938372 0.02 -3.189242 2.674833 8.666433 0.0005417 0.0673263 0.0000246 4176.5 8.337229 8.724207 0.02 -3.933692 0.033033 6.955763 0.0007694 0.0511216 0.0000195 157.0 5.056246 9.752665 0.02 -5.271388 -7.016106 8.277811 0.0009076 0.0120942 0.0000222 pass 173 0.0001780 5617.6079 44 3.91e-05 13024 0.02 244.5 0.0000706 14172.4198 161 3.91e-05 24023.5 0.02 1211 0.0004337 2305.9691 121.5 3.91e-05 23687 0.02 717 0.0002429 4117.2930 116 3.91e-05 17664 0.02 1808.0 0.0011610 861.3537 86 3.91e-05 9648 0.02 164.0 0.0002189 4567.835 29 3.91e-05 13146.5 0.02 242 0.0002389 4185.4929 52.5 3.91e-05 14354 0.02 640.0 0.0001721 5809.2375 167 3.91e-05 24512 0.02 292 0.0021690 461.0490 26 3.91e-05 792.5 0.02 243.0 0.0003928 2545.6460 42 3.91e-05 2658 0.02 243.0 0.0012954 771.9617 23.5 3.91e-05 1009 0.02 213.5 0.0039961 250.24363 15 3.91e-05 438 0.02 410.0 0.0000862 11600.8858 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 0.0002677 0.0001188 0.0000195 0.0001852 0.0009249 0.0006430 0.0019237 0.0011044 0.0200000 0.0007167 0.0011269 0.0004915 0.0200000 0.0022294 0.0200000 0.0200000 0.0014803 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 0.0000670 0.0000222 0.0000195 0.0000331 0.0003251 0.0001129 0.0001926 0.0001220 0.0004303 0.0003277 0.0004604 0.0000843 0.0032324 0.0006608 0.0037564 0.0136755 0.0003596 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 0.0001441 0.0009517 0.0000195 0.0002067 0.0000871 0.0001926 0.0003623 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 0.0000629 0.0000699 0.0002013 0.0000195 0.0007167 0.0015092 0.0001013 0.0003335 0.0019523 0.0002732 0.0003984 0.0011290 0.0016733 0.0022394 0.0015668 0.0045507 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 0.0002956 0.0001132 0.0000195 0.0002089 0.0012828 0.0007212 0.0008246 0.0011130 0.0200000 0.0016951 0.0014241 0.0008983 0.0200000 0.0015870 0.0200000 0.0200000 0.0010250 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 0.0000412 0.0000246 0.0000195 0.0000222 0.0001780 0.0000706 0.0004337 0.0002429 0.0011610 0.0002189 0.0002389 0.0001721 0.0021690 0.0003928 0.0012954 0.0039961 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 0.0002677 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 0.0001852 loglog
ABC-0001 plate1 Pv-fam-a Pv 1020.0 0.0009249 loglog
ABC-0001 plate1 Pv-fam-a Pv 1020.0 0.0010659 Adj_loglog