Pearson’s Chi square test or Fisher’s exact test (in case of too few expected events) was used to evaluate categorical data (for example, prior treatment versus the occurrence of a certain mutation). To compare continuous variables (for example the relative contribution of mutational signatures versus breast cancer subtype or RECIST1.1 response category (CR/PR or PD)) a Mann-Whitney U-test or a Kruskal-Wallis H-test was performed. Where suitable, effect sizes and confidence intervals were estimated using Hodges-Lehmann’s method48 ,49 (link). All statistical tests were two-sided and considered statistically significant when P <0.05. Stata 13.0 software, R version 3.4.4. or SPSS version 24 were used for the statistical analyses. We used the Hochberg procedure to correct p-values for multiple hypothesis testing when appropriate.
R version 3.4.4
Manufactured by IBM
Sourced in United States
R is a free, open-source software environment for statistical computing and graphics. It is widely used for data analysis, statistical modeling, and visualization. Version 3.4.4 provides a stable and reliable platform for various statistical and data manipulation tasks.
Automatically generated - may contain errors
Lab products found in correlation
4 protocols using r version 3.4.4
1
Statistical Analysis of Molecular Profiles
2
Correlating Genomic and Metabolic Features
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Association between these genomic and tumor metabolic features was analyzed by using correlation analysis and the prognostic value of the parameters were assessed using the log-rank test. To analyze the correlation between two genomic and selected six FDG PET features, Spearman correlation analysis was performed. Correlation coefficients and p values were gained and used to sort statistically significant features (P value < 0.05). All statistical analyses were performed in R (version 3.4.4) and SPSS (version 25). All tests were two-sided and P values less than 0.05 were considered significant.
3
Molecular Subtype Analysis of 18F-FDG PET and Immune Signatures
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Comparisons of clinical variables, the cytolytic score and the 18F-FDG PET parameters according to the molecular subtype were done by Chi-square tests and ANOVA tests. A correlation analysis between the 18F-FDG PET parameters, immune signatures and immune cells was conducted by means of a Pearson correlation analysis. The patients were divided into low and high groups according to the median value of each continuous variable for a survival analysis. In the survival analysis, high and low groups were assessed by a Kaplan–Meier survival analysis and a log-rank test. To assess the stratified prognostic value further, a Cox multivariate regression analysis was done using the 18F-FDG PET parameters and immune cells. All statistical analyses were two-sided, and P values less than 0.05 were regarded as significant. These analyses were performed with R (version 3.4.4) and SPSS (version 25).
4
Melatonin Synthesis Associations and Prognosis
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Associations between melatonin synthesis/metabolism subgroups and categorical variables (eg, sex, race, and disease stage) were analyzed using the chi-square test (Fisher's exact test or Pearson's chi-square test where appropriate), and the Mann-Whitney U test or Kruskal-Wallis test for continuous variables (eg, age, number of mutations, and neoantigens). Correlations between gene expression were evaluated using the Spearman correlation test; the Spearman coefficient was considered to indicate poor correlation if <0.2, moderate if <0.4, relatively strong if <0.6, strong if <0.8, and very strong if >0.8. The prognostic significance of the indexes was estimated using Kaplan-Meier survival curves and compared by log-rank test. Cox proportional hazards model was used to calculate the adjusted hazard ratios (AHRs) and corresponding 95% confidence intervals (CIs), incorporating age, sex, race, and disease stage for adjustment. All statistical analyses were performed with SPSS version 23.0 (SPSS Inc, Chicago, IL, USA) and R version 3.4.4 (http://www.r-project.org). Statistical significance was set at two-sided P < 0.05.
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