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 -0.2551942 1.721839 14.738 0.0020263 1.430763 0.0017050 346.0 5.846439 9.847314 0.02 -0.6004033 5.697488 10.13619 5.82e-05 2.423488 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 -0.3905888 2.274053 9.060852 6.63e-05 2.808942 0.0019575 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 10352.512 149 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 0.0007857 0.0021518 0.0016640 0.0046023 0.0009566 0.0008755 0.0011163 0.0008338
ABC-0002 14(1,B2) B2 Unknown14 plate1 344 5.840642 8.631057 0.02 -0.2551942 1.721839 14.738 0.0020263 1.430763 0.0008863 228.5 5.431536 9.847314 0.02 -0.6004033 5.697488 10.13619 5.82e-05 2.423488 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 -0.3905888 2.274053 9.060852 6.63e-05 2.808942 0.0005508 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 19298.140 149 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 0.0006031 0.0015663 0.0012893 0.0038369 0.0012443 0.0007377 0.0007054 0.0006522
ABC-0003 15(1,B3) B3 Unknown15 plate1 716 6.573680 8.631057 0.02 -0.2551942 1.721839 14.738 0.0020263 1.430763 0.0020814 584.0 6.369901 9.847314 0.02 -0.6004033 5.697488 10.13619 5.82e-05 2.423488 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 -0.3905888 2.274053 9.060852 6.63e-05 2.808942 0.0015955 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 0.0010225 0.0027924 0.0021826 0.0052246 0.0012934 0.0009877 0.0013651 0.0010920
ABC-0004 16(1,B4) B4 Unknown16 plate1 357 5.877736 8.631057 0.02 -0.2551942 1.721839 14.738 0.0020263 1.430763 0.0009267 235.0 5.459586 9.847314 0.02 -0.6004033 5.697488 10.13619 5.82e-05 2.423488 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 -0.3905888 2.274053 9.060852 6.63e-05 2.808942 0.0007401 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 15768.910 149 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 0.0006579 0.0016485 0.0014020 0.0037384 0.0007542 0.0007730 0.0008111 0.0006859
ABC-0005 17(1,B5) B5 Unknown17 plate1 1320 7.185387 8.631057 0.02 -0.2551942 1.721839 14.738 0.0020263 1.430763 0.0041184 746.0 6.614726 9.847314 0.02 -0.6004033 5.697488 10.13619 5.82e-05 2.423488 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 -0.3905888 2.274053 9.060852 6.63e-05 2.808942 0.0063403 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 0.0011839 0.0030464 0.0025434 0.0076085 0.0015785 0.0012407 0.0013608 0.0012346
ABC-0006 18(1,B6) B6 Unknown18 plate1 899 6.801283 8.631057 0.02 -0.2551942 1.721839 14.738 0.0020263 1.430763 0.0026892 733.0 6.597146 9.847314 0.02 -0.6004033 5.697488 10.13619 5.82e-05 2.423488 6.54e-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 -0.3905888 2.274053 9.060852 6.63e-05 2.808942 0.0094388 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 0.0011651 0.0028932 0.0025479 0.0059766 0.0038660 0.0011178 0.0012736 0.0012203

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 0.0019575 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 0.0007857 0.0021518 0.0016640 0.0046023 0.0009566 0.0008755 0.0011163 0.0008338
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 0.0005508 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 0.0006031 0.0015663 0.0012893 0.0038369 0.0012443 0.0007377 0.0007054 0.0006522
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 0.0015955 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 0.0010225 0.0027924 0.0021826 0.0052246 0.0012934 0.0009877 0.0013651 0.0010920
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 0.0007401 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 0.0006579 0.0016485 0.0014020 0.0037384 0.0007542 0.0007730 0.0008111 0.0006859
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 0.0063403 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 0.0011839 0.0030464 0.0025434 0.0076085 0.0015785 0.0012407 0.0013608 0.0012346
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 6.54e-05 0.0024374 0.0094388 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 0.0011651 0.0028932 0.0025479 0.0059766 0.0038660 0.0011178 0.0012736 0.0012203

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 0.0019575 loglog
ABC-0001 plate1 Pv-fam-a NA 389 0.0000834 loglog
ABC-0001 plate1 Pv-fam-a NA 389 0.0021518 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 -3.51772 -5.449795 8.563904 0.0006497 0.0231174 2.68e-04 1095.0 6.998510 9.938372 0.02 -3.189257 2.674807 8.666433 0.0005417 0.0673256 0.0001188 5761.0 8.658866 8.724207 0.02 -3.933695 0.0330283 6.955762 0.0007694 0.0511214 0.0000195 901.5 6.804060 9.752665 0.02 -3.129037 0.1037915 8.270118 0.0007188 0.0456963 0.0001809 pass 1020 0.0009250 1081.1273 44 3.91e-05 13024 0.02 1987.0 0.0006429 1555.3802 161 3.91e-05 24023.5 0.02 5070 0.0019240 519.7601 121.5 3.91e-05 23687 0.02 3140 0.0011049 905.0766 116 3.91e-05 17664 0.02 15170.0 0.0200000 50.0000 86 3.91e-05 9648 0.02 672.0 0.0007174 1393.9789 29 3.91e-05 13146.5 0.02 1350 0.0011264 887.7506 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 0.0014819 674.7885 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 -3.51772 -5.449795 8.563904 0.0006497 0.0231174 6.70e-05 296.5 5.692047 9.938372 0.02 -3.189257 2.674807 8.666433 0.0005417 0.0673256 0.0000222 4583.0 8.430109 8.724207 0.02 -3.933695 0.0330283 6.955762 0.0007694 0.0511214 0.0000195 214.5 5.368310 9.752665 0.02 -3.129037 0.1037915 8.270118 0.0007188 0.0456963 0.0000334 pass 329 0.0003250 3077.2102 44 3.91e-05 13024 0.02 369.5 0.0001128 8864.7593 161 3.91e-05 24023.5 0.02 521 0.0001926 5193.1622 121.5 3.91e-05 23687 0.02 346 0.0001219 8200.6370 116 3.91e-05 17664 0.02 778.0 0.0004303 2324.0862 86 3.91e-05 9648 0.02 264.5 0.0003277 3051.9223 29 3.91e-05 13146.5 0.02 500 0.0004605 2171.3223 52.5 3.91e-05 14354 0.02 324.0 0.0000843 11861.3051 167 3.91e-05 24512 0.02 364 0.0032324 309.3700 26 3.91e-05 792.5 0.02 366.0 0.0006612 1512.4952 42 3.91e-05 2658 0.02 462.5 0.0037578 266.1167 23.5 3.91e-05 1009 0.02 368.5 0.0136944 73.02272 15 3.91e-05 438 0.02 1003.5 0.0003596 2780.5551 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 -3.51772 -5.449795 8.563904 0.0006497 0.0231174 1.95e-05 36.0 3.583519 9.938372 0.02 -3.189257 2.674807 8.666433 0.0005417 0.0673256 0.0000195 465.0 6.142037 8.724207 0.02 -3.933695 0.0330283 6.955762 0.0007694 0.0511214 0.0004228 63.0 4.143135 9.752665 0.02 -3.129037 0.1037915 8.270118 0.0007188 0.0456963 0.0000195 pass 64 0.0000636 15719.9263 44 3.91e-05 13024 0.02 50.0 0.0000195 51200.0000 161 3.91e-05 24023.5 0.02 113 0.0000376 26614.7105 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 0.0001439 6950.7151 29 3.91e-05 13146.5 0.02 1124 0.0009514 1051.0596 52.5 3.91e-05 14354 0.02 52.0 0.0000195 51200.0000 167 3.91e-05 24512 0.02 66 0.0002067 4838.8208 26 3.91e-05 792.5 0.02 75.0 0.0000871 11484.8776 42 3.91e-05 2658 0.02 64.0 0.0001930 5182.2186 23.5 3.91e-05 1009 0.02 60.0 0.0003625 2758.34679 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 -3.51772 -5.449795 8.563904 0.0006497 0.0231174 6.29e-05 688.5 6.534515 9.938372 0.02 -3.189257 2.674807 8.666433 0.0005417 0.0673256 0.0000699 204.0 5.318120 8.724207 0.02 -3.933695 0.0330283 6.955762 0.0007694 0.0511214 0.0002013 6687.0 8.807921 9.752665 0.02 -3.129037 0.1037915 8.270118 0.0007188 0.0456963 0.0000195 pass 777 0.0007167 1395.3209 44 3.91e-05 13024 0.02 4357.0 0.0015106 661.9674 161 3.91e-05 24023.5 0.02 273 0.0001013 9872.3977 121.5 3.91e-05 23687 0.02 998 0.0003334 2999.4431 116 3.91e-05 17664 0.02 2673.0 0.0019523 512.2274 86 3.91e-05 9648 0.02 213.0 0.0002731 3661.1820 29 3.91e-05 13146.5 0.02 425 0.0003985 2509.3100 52.5 3.91e-05 14354 0.02 3718.0 0.0011290 885.7238 167 3.91e-05 24512 0.02 251 0.0016733 597.6161 26 3.91e-05 792.5 0.02 876.0 0.0022385 446.7223 42 3.91e-05 2658 0.02 275.0 0.0015653 638.8740 23.5 3.91e-05 1009 0.02 227.0 0.0045414 220.19532 15 3.91e-05 438 0.02 499.0 0.0001171 8540.4077 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 -3.51772 -5.449795 8.563904 0.0006497 0.0231174 2.96e-04 1047.5 6.954162 9.938372 0.02 -3.189257 2.674807 8.666433 0.0005417 0.0673256 0.0001132 1563.0 7.354362 8.724207 0.02 -3.933695 0.0330283 6.955762 0.0007694 0.0511214 0.0000195 1002.5 6.910252 9.752665 0.02 -3.129037 0.1037915 8.270118 0.0007188 0.0456963 0.0002023 pass 1434 0.0012830 779.4469 44 3.91e-05 13024 0.02 2218.0 0.0007213 1386.4012 161 3.91e-05 24023.5 0.02 2318 0.0008244 1213.0476 121.5 3.91e-05 23687 0.02 3161 0.0011134 898.1117 116 3.91e-05 17664 0.02 14703.5 0.0200000 50.0000 86 3.91e-05 9648 0.02 1764.5 0.0016964 589.4908 29 3.91e-05 13146.5 0.02 1730 0.0014233 702.6090 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 630.1706 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 0.0010259 974.7593 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 -3.51772 -5.449795 8.563904 0.0006497 0.0231174 4.12e-05 317.0 5.758902 9.938372 0.02 -3.189257 2.674807 8.666433 0.0005417 0.0673256 0.0000246 4176.5 8.337229 8.724207 0.02 -3.933695 0.0330283 6.955762 0.0007694 0.0511214 0.0000195 157.0 5.056246 9.752665 0.02 -3.129037 0.1037915 8.270118 0.0007188 0.0456963 0.0000218 pass 173 0.0001779 5619.7927 44 3.91e-05 13024 0.02 244.5 0.0000705 14175.7561 161 3.91e-05 24023.5 0.02 1211 0.0004335 2306.8481 121.5 3.91e-05 23687 0.02 717 0.0002428 4118.9106 116 3.91e-05 17664 0.02 1808.0 0.0011610 861.3537 86 3.91e-05 9648 0.02 164.0 0.0002188 4571.2927 29 3.91e-05 13146.5 0.02 242 0.0002391 4182.2418 52.5 3.91e-05 14354 0.02 640.0 0.0001721 5809.2375 167 3.91e-05 24512 0.02 292 0.0021690 461.0521 26 3.91e-05 792.5 0.02 243.0 0.0003930 2544.3710 42 3.91e-05 2658 0.02 243.0 0.0012939 772.8387 23.5 3.91e-05 1009 0.02 213.5 0.0039875 250.78406 15 3.91e-05 438 0.02 410.0 0.0000862 11606.3571 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 2.68e-04 0.0001188 0.0000195 0.0001809 0.0009250 0.0006429 0.0019240 0.0011049 0.0200000 0.0007174 0.0011264 0.0004915 0.0200000 0.0022286 0.0200000 0.0200000 0.0014819 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 6.70e-05 0.0000222 0.0000195 0.0000334 0.0003250 0.0001128 0.0001926 0.0001219 0.0004303 0.0003277 0.0004605 0.0000843 0.0032324 0.0006612 0.0037578 0.0136944 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 1.95e-05 0.0000195 0.0004228 0.0000195 0.0000636 0.0000195 0.0000376 0.0000195 0.0003985 0.0001439 0.0009514 0.0000195 0.0002067 0.0000871 0.0001930 0.0003625 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 6.29e-05 0.0000699 0.0002013 0.0000195 0.0007167 0.0015106 0.0001013 0.0003334 0.0019523 0.0002731 0.0003985 0.0011290 0.0016733 0.0022385 0.0015653 0.0045414 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 2.96e-04 0.0001132 0.0000195 0.0002023 0.0012830 0.0007213 0.0008244 0.0011134 0.0200000 0.0016964 0.0014233 0.0008983 0.0200000 0.0015869 0.0200000 0.0200000 0.0010259 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 4.12e-05 0.0000246 0.0000195 0.0000218 0.0001779 0.0000705 0.0004335 0.0002428 0.0011610 0.0002188 0.0002391 0.0001721 0.0021690 0.0003930 0.0012939 0.0039875 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 0.0002680 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 NA 1020.0 0.0009250 loglog
ABC-0001 plate1 Pv-fam-a NA 1020.0 0.0010659 Adj_loglog