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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 -0.2551645 1.721586 14.73931 0.0020267 1.430804 0.0017051 346.0 5.846439 9.847314 0.02 -0.6012387 5.702389 10.13445 5.79e-05 2.436915 1.95e-05 858.0 6.754604 9.278139 0.02 -0.1799282 -7.458125 13.42812 5.16e-05 0.7583175 0.0005132 320.0 5.768321 7.38399 0.02 -0.3947068 2.251795 9.04416 8.37e-05 2.600622 0.0019585 pass 389.0 0.0000834 11989.153 159 3.2e-05 17367 0.02 392 0.0000856 11684.572 174.5 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 25004.970 713 3.2e-05 23660.5 0.02 438.0 0.0007845 1274.6183 37 3.2e-05 6152 0.02 556.0 0.0007195 1389.7801 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 0.0000064 0.0001358 0.0002014 1.07e-05
ABC-0002 14(1,B2) B2 Unknown14 plate1 344 5.840642 8.631057 0.02 -0.2551645 1.721586 14.73931 0.0020267 1.430804 0.0008863 228.5 5.431536 9.847314 0.02 -0.6012387 5.702389 10.13445 5.79e-05 2.436915 1.95e-05 384.0 5.950643 9.278139 0.02 -0.1799282 -7.458125 13.42812 5.16e-05 0.7583175 0.0001859 112.5 4.722953 7.38399 0.02 -0.3947068 2.251795 9.04416 8.37e-05 2.600622 0.0005510 pass 217.0 0.0000441 22679.984 159 3.2e-05 17367 0.02 242 0.0000477 20961.434 174.5 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 50274.271 713 3.2e-05 23660.5 0.02 171.0 0.0002491 4014.0621 37 3.2e-05 6152 0.02 377.0 0.0004552 2196.6087 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 0.0000103 0.0000384 0.0000281 0.0000566 0.0000064 0.0000865 0.0000687 8.10e-06
ABC-0003 15(1,B3) B3 Unknown15 plate1 716 6.573680 8.631057 0.02 -0.2551645 1.721586 14.73931 0.0020267 1.430804 0.0020815 584.0 6.369901 9.847314 0.02 -0.6012387 5.702389 10.13445 5.79e-05 2.436915 4.43e-05 4397.0 8.388678 9.278139 0.02 -0.1799282 -7.458125 13.42812 5.16e-05 0.7583175 0.0049897 271.0 5.602119 7.38399 0.02 -0.3947068 2.251795 9.04416 8.37e-05 2.600622 0.0015964 pass 634.0 0.0001442 6936.335 159 3.2e-05 17367 0.02 663 0.0001605 6231.025 174.5 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 0.0000778 12854.231 713 3.2e-05 23660.5 0.02 671.0 0.0013071 765.0369 37 3.2e-05 6152 0.02 731.5 0.0009980 1001.9781 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 0.0000064 0.0001867 0.0003170 3.09e-05
ABC-0004 16(1,B4) B4 Unknown16 plate1 357 5.877736 8.631057 0.02 -0.2551645 1.721586 14.73931 0.0020267 1.430804 0.0009267 235.0 5.459586 9.847314 0.02 -0.6012387 5.702389 10.13445 5.79e-05 2.436915 1.95e-05 437.5 6.081077 9.278139 0.02 -0.1799282 -7.458125 13.42812 5.16e-05 0.7583175 0.0002185 143.5 4.966335 7.38399 0.02 -0.3947068 2.251795 9.04416 8.37e-05 2.600622 0.0007405 pass 238.0 0.0000487 20520.215 159 3.2e-05 17367 0.02 283 0.0000578 17311.538 174.5 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 0.0000232 43028.511 713 3.2e-05 23660.5 0.02 226.0 0.0003518 2842.7736 37 3.2e-05 6152 0.02 419.0 0.0005153 1940.7124 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 0.0000114 0.0000484 0.0000408 0.0000542 0.0000064 0.0000978 0.0000959 8.50e-06
ABC-0005 17(1,B5) B5 Unknown17 plate1 1320 7.185387 8.631057 0.02 -0.2551645 1.721586 14.73931 0.0020267 1.430804 0.0041185 746.0 6.614726 9.847314 0.02 -0.6012387 5.702389 10.13445 5.79e-05 2.436915 6.73e-05 1620.0 7.390181 9.278139 0.02 -0.1799282 -7.458125 13.42812 5.16e-05 0.7583175 0.0011931 778.0 6.656727 7.38399 0.02 -0.3947068 2.251795 9.04416 8.37e-05 2.600622 0.0063390 pass 746.0 0.0001737 5757.718 159 3.2e-05 17367 0.02 892 0.0002296 4356.195 174.5 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 0.0001039 9627.667 713 3.2e-05 23660.5 0.02 666.5 0.0012967 771.2116 37 3.2e-05 6152 0.02 1220.5 0.0018571 538.4811 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 -0.2551645 1.721586 14.73931 0.0020267 1.430804 0.0026892 733.0 6.597146 9.847314 0.02 -0.6012387 5.702389 10.13445 5.79e-05 2.436915 6.55e-05 2702.5 7.901933 9.278139 0.02 -0.1799282 -7.458125 13.42812 5.16e-05 0.7583175 0.0024371 1015.0 6.922644 7.38399 0.02 -0.3947068 2.251795 9.04416 8.37e-05 2.600622 0.0094354 pass 677.5 0.0001555 6430.683 159 3.2e-05 17367 0.02 895 0.0002305 4338.452 174.5 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 0.0001011 9893.620 713 3.2e-05 23660.5 0.02 579.0 0.0010959 912.4657 37 3.2e-05 6152 0.02 967.5 0.0013985 715.0615 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 0.0017051 1.95e-05 0.0005132 0.0019585 0.0000834 0.0000856 1.95e-05 0.0000966 0.0000400 0.0007845 0.0007195 0.0000233 0.0004380 0.0011172 0.0050186 0.0061629 0.0052569 0.0000258 0.0000923 0.0000800 0.0000762 0.0000064 0.0001358 0.0002014 1.07e-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 0.0001859 0.0005510 0.0000441 0.0000477 1.95e-05 0.0000518 0.0000199 0.0002491 0.0004552 0.0000423 0.0002323 0.0006105 0.0031701 0.0038047 0.0026246 0.0000103 0.0000384 0.0000281 0.0000566 0.0000064 0.0000865 0.0000687 8.10e-06
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 0.0020815 4.43e-05 0.0049897 0.0015964 0.0001442 0.0001605 1.95e-05 0.0001845 0.0000778 0.0013071 0.0009980 0.0000463 0.0009122 0.0020438 0.0112317 0.0114129 0.0120404 0.0000784 0.0001591 0.0001564 0.0000969 0.0000064 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 0.0002185 0.0007405 0.0000487 0.0000578 1.95e-05 0.0000634 0.0000232 0.0003518 0.0005153 0.0000195 0.0002796 0.0007440 0.0032063 0.0039019 0.0037705 0.0000114 0.0000484 0.0000408 0.0000542 0.0000064 0.0000978 0.0000959 8.50e-06
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 0.0041185 6.73e-05 0.0011931 0.0063390 0.0001737 0.0002296 1.95e-05 0.0002673 0.0001039 0.0012967 0.0018571 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 0.0024371 0.0094354 0.0001555 0.0002305 1.95e-05 0.0002566 0.0001011 0.0010959 0.0013985 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 0.0017051 loglog
ABC-0001 plate1 PkMSP10 Pk 346 0.0000195 loglog
ABC-0001 plate1 PkSERA3Ag2 Pk 858 0.0005132 loglog
ABC-0001 plate1 PkSSP2 Pk 320 0.0019585 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 -3.9205 -8.461397 8.564957 0.0006842 0.0163902 0.0002717 1095.0 6.998510 9.938372 0.02 -3.189269 2.674789 8.666433 0.0005417 0.067325 0.0001188 5761.0 8.658866 8.724207 0.02 -3.933689 0.0330382 6.955764 0.0007694 0.0511217 0.0000195 901.5 6.804060 9.752665 0.02 -3.139519 0.0833707 8.270251 0.0007204 0.0453669 0.0001810 pass 1020 0.0009255 1080.4904 44 3.91e-05 13024 0.02 1987.0 0.0006431 1555.0851 161 3.91e-05 24023.5 0.02 5070 0.0019234 519.9138 121.5 3.91e-05 23687 0.02 3140 0.0011043 905.5877 116 3.91e-05 17664 0.02 15170.0 0.0200000 50.0000 86 3.91e-05 9648 0.02 672.0 0.0007167 1395.2843 29 3.91e-05 13146.5 0.02 1350 0.0011282 886.4050 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 0.0022302 448.3979 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 0.0014832 674.2052 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 -3.9205 -8.461397 8.564957 0.0006842 0.0163902 0.0000667 296.5 5.692047 9.938372 0.02 -3.189269 2.674789 8.666433 0.0005417 0.067325 0.0000222 4583.0 8.430109 8.724207 0.02 -3.933689 0.0330382 6.955764 0.0007694 0.0511217 0.0000195 214.5 5.368310 9.752665 0.02 -3.139519 0.0833707 8.270251 0.0007204 0.0453669 0.0000333 pass 329 0.0003250 3077.2068 44 3.91e-05 13024 0.02 369.5 0.0001129 8854.6989 161 3.91e-05 24023.5 0.02 521 0.0001926 5191.1715 121.5 3.91e-05 23687 0.02 346 0.0001220 8194.5088 116 3.91e-05 17664 0.02 778.0 0.0004303 2324.0862 86 3.91e-05 9648 0.02 264.5 0.0003277 3051.9783 29 3.91e-05 13146.5 0.02 500 0.0004603 2172.5611 52.5 3.91e-05 14354 0.02 324.0 0.0000843 11861.3051 167 3.91e-05 24512 0.02 364 0.0032324 309.3699 26 3.91e-05 792.5 0.02 366.0 0.0006607 1513.6448 42 3.91e-05 2658 0.02 462.5 0.0037539 266.3904 23.5 3.91e-05 1009 0.02 368.5 0.0136762 73.11951 15 3.91e-05 438 0.02 1003.5 0.0003597 2780.0023 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 -3.9205 -8.461397 8.564957 0.0006842 0.0163902 0.0000195 36.0 3.583519 9.938372 0.02 -3.189269 2.674789 8.666433 0.0005417 0.067325 0.0000195 465.0 6.142037 8.724207 0.02 -3.933689 0.0330382 6.955764 0.0007694 0.0511217 0.0004228 63.0 4.143135 9.752665 0.02 -3.139519 0.0833707 8.270251 0.0007204 0.0453669 0.0000195 pass 64 0.0000636 15730.1857 44 3.91e-05 13024 0.02 50.0 0.0000195 51200.0000 161 3.91e-05 24023.5 0.02 113 0.0000375 26640.8495 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 6940.4767 29 3.91e-05 13146.5 0.02 1124 0.0009526 1049.7805 52.5 3.91e-05 14354 0.02 52.0 0.0000195 51200.0000 167 3.91e-05 24512 0.02 66 0.0002067 4838.8218 26 3.91e-05 792.5 0.02 75.0 0.0000871 11477.5135 42 3.91e-05 2658 0.02 64.0 0.0001931 5178.9448 23.5 3.91e-05 1009 0.02 60.0 0.0003621 2761.35844 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 -3.9205 -8.461397 8.564957 0.0006842 0.0163902 0.0000626 688.5 6.534515 9.938372 0.02 -3.189269 2.674789 8.666433 0.0005417 0.067325 0.0000699 204.0 5.318120 8.724207 0.02 -3.933689 0.0330382 6.955764 0.0007694 0.0511217 0.0002013 6687.0 8.807921 9.752665 0.02 -3.139519 0.0833707 8.270251 0.0007204 0.0453669 0.0000195 pass 777 0.0007171 1394.5361 44 3.91e-05 13024 0.02 4357.0 0.0015096 662.4055 161 3.91e-05 24023.5 0.02 273 0.0001013 9871.9536 121.5 3.91e-05 23687 0.02 998 0.0003335 2998.8227 116 3.91e-05 17664 0.02 2673.0 0.0019523 512.2274 86 3.91e-05 9648 0.02 213.0 0.0002732 3660.0388 29 3.91e-05 13146.5 0.02 425 0.0003981 2511.7890 52.5 3.91e-05 14354 0.02 3718.0 0.0011290 885.7238 167 3.91e-05 24512 0.02 251 0.0016733 597.6160 26 3.91e-05 792.5 0.02 876.0 0.0022401 446.4104 42 3.91e-05 2658 0.02 275.0 0.0015643 639.2641 23.5 3.91e-05 1009 0.02 227.0 0.0045510 219.73379 15 3.91e-05 438 0.02 499.0 0.0001171 8542.4231 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 -3.9205 -8.461397 8.564957 0.0006842 0.0163902 0.0003004 1047.5 6.954162 9.938372 0.02 -3.189269 2.674789 8.666433 0.0005417 0.067325 0.0001132 1563.0 7.354362 8.724207 0.02 -3.933689 0.0330382 6.955764 0.0007694 0.0511217 0.0000195 1002.5 6.910252 9.752665 0.02 -3.139519 0.0833707 8.270251 0.0007204 0.0453669 0.0002024 pass 1434 0.0012836 779.0458 44 3.91e-05 13024 0.02 2218.0 0.0007213 1386.3178 161 3.91e-05 24023.5 0.02 2318 0.0008245 1212.8643 121.5 3.91e-05 23687 0.02 3161 0.0011128 898.6214 116 3.91e-05 17664 0.02 14703.5 0.0200000 50.0000 86 3.91e-05 9648 0.02 1764.5 0.0016951 589.9337 29 3.91e-05 13146.5 0.02 1730 0.0014259 701.3179 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 0.0015872 630.0426 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 0.0010267 974.0294 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 -3.9205 -8.461397 8.564957 0.0006842 0.0163902 0.0000410 317.0 5.758902 9.938372 0.02 -3.189269 2.674789 8.666433 0.0005417 0.067325 0.0000246 4176.5 8.337229 8.724207 0.02 -3.933689 0.0330382 6.955764 0.0007694 0.0511217 0.0000195 157.0 5.056246 9.752665 0.02 -3.139519 0.0833707 8.270251 0.0007204 0.0453669 0.0000217 pass 173 0.0001778 5623.7989 44 3.91e-05 13024 0.02 244.5 0.0000706 14172.2711 161 3.91e-05 24023.5 0.02 1211 0.0004337 2305.9389 121.5 3.91e-05 23687 0.02 717 0.0002429 4117.0589 116 3.91e-05 17664 0.02 1808.0 0.0011610 861.3537 86 3.91e-05 9648 0.02 164.0 0.0002189 4567.9171 29 3.91e-05 13146.5 0.02 242 0.0002385 4192.3152 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 0.0003927 2546.5487 42 3.91e-05 2658 0.02 243.0 0.0012933 773.1874 23.5 3.91e-05 1009 0.02 213.5 0.0039963 250.23298 15 3.91e-05 438 0.02 410.0 0.0000861 11609.1146 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 0.0002717 0.0001188 0.0000195 0.0001810 0.0009255 0.0006431 0.0019234 0.0011043 0.0200000 0.0007167 0.0011282 0.0004915 0.0200000 0.0022302 0.0200000 0.0200000 0.0014832 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 0.0000667 0.0000222 0.0000195 0.0000333 0.0003250 0.0001129 0.0001926 0.0001220 0.0004303 0.0003277 0.0004603 0.0000843 0.0032324 0.0006607 0.0037539 0.0136762 0.0003597 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 0.0009526 0.0000195 0.0002067 0.0000871 0.0001931 0.0003621 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 0.0000626 0.0000699 0.0002013 0.0000195 0.0007171 0.0015096 0.0001013 0.0003335 0.0019523 0.0002732 0.0003981 0.0011290 0.0016733 0.0022401 0.0015643 0.0045510 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 0.0003004 0.0001132 0.0000195 0.0002024 0.0012836 0.0007213 0.0008245 0.0011128 0.0200000 0.0016951 0.0014259 0.0008983 0.0200000 0.0015872 0.0200000 0.0200000 0.0010267 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 0.0000217 0.0001778 0.0000706 0.0004337 0.0002429 0.0011610 0.0002189 0.0002385 0.0001721 0.0021690 0.0003927 0.0012933 0.0039963 0.0000861 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 0.0002717 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 0.0001810 loglog
ABC-0001 plate1 Pv-fam-a Pv 1020.0 0.0009255 loglog
ABC-0001 plate1 Pv-fam-a Pv 1020.0 0.0010659 Adj_loglog