Computational protocol: Cytokine and chemokine profile of the innate and adaptive immune response of schistosoma haematobium and plasmodium falciparum single and co-infected school-aged children from an endemic area of Lambaréné, Gabon

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Protocol publication

[…] Chi square and fisher’s exact test were used to compare categorical variables. Not normally distributed quantitative variables were transformed either by Log10 or Box-Cox transformation. Student t-test and ANOVA were performed when data met the assumption of normality. Otherwise the non-parametric Mann Whitney and Kruskal Wallis tests were used. Correlation between two continuous variables was assessed using the spearman rho test.Principal component analysis (PCA) was carried out on the cytokine variables in order to summarize them. Of note PCA is a mathematical technique that allows reducing the dimension of large dataset by identifying new summary variables also called principal component (PC). Each principal component is made of a set of original variables that share a certain level of correlation. All the analysis was performed on medium subtracted data. Negative values were set to zero. Cytokine from the innate [obtained after whole blood stimulation] and the adaptive panels [obtained after PBMC stimulation] were analyzed independently by PCA. As mentioned above the innate panel consisted of 12 cytokines measured after stimulation of cells by six different conditions. Before performing the PCA an average cytokine response were calculated for each subject by taking the mean of the cytokine level obtained with the six different stimuli. This step only concerned the innate panel and was not needed for cytokine of the adaptive panel since the cytokine response to one stimulus was only assessed. All variables were transformed either using a log10 or a Box-Cox transformation to reduce skewness prior to PCA. Principal components identified were considered for further analysis if their eigenvalues were above one. No rotation was applied. Individuals PC scores were obtained for each subject and used for comparison between groups. All the statistical tests were computed using R version 3.0.1. The R packages ggplot2 version 0.9.3.1 and FactoMineR version 1.25 were used for making graphs and performing the PCA respectively. Statistical significance was set for p value below 0.05. […]

Pipeline specifications

Software tools Ggplot2, FactoMineR
Application Miscellaneous
Organisms Schistosoma haematobium, Plasmodium falciparum, Homo sapiens
Diseases Communicable Diseases, Infection, Malaria, Malaria, Falciparum