ImmuneSpaceR code produces consistent results, regardless of whether it is being executed from a module or UI based report on the server or on a local machine. This vignette reproduces a report available on the ImmuneSpace portal using the same code.
This report investigate the association between the number influenza-specific cells measured by ELISPOT measured at day 7 with the number of plasmablast measured by flow cytometry and day 7 and the HAI response measured at day 28 (log-fold day28/day0). It basically reproduces Figure 1 d-e) of Nakaya et al. (2011) published as part of the original study.
# Compute max fold change for HAI, and remove time zero dt_hai <- dt_hai[, hai_response := value_preferred / value_preferred[study_time_collected == 0], by = "virus,cohort,participant_id"][study_time_collected == 28] dt_hai <- dt_hai[, list(hai_response = max(hai_response)), by = "cohort,participant_id"] # Define variable for ELISPOT, keep only the IgG class dt_elispot <- dt_elispot[, elispot_response := spot_number_reported + 1][study_time_collected == 7 & analyte == "IgG"] # Compute % plasmablasts dt_fcs <- dt_fcs[, fcs_response := (as.double(population_cell_number) + 1) / as.double(base_parent_population)][study_time_collected == 7]
The figure below shows the absolute number of plasmablast cells measured by flow cytometry vs. the number of frequency of influenza-specific cells measured by ELISPOT.
The figure below shows the HAI fold increase over baseline vs. the number of frequency of influenza-specific cells measured by ELISPOT.
In each case, we observe good correlations between the different responses, at least for the TIV cohort.