Question
A simulated gene expression data set (gene_expression.csv), I couldn't upload the data set but it includes two groups - normal group and cancer group .
A simulated gene expression data set (gene_expression.csv), I couldn't upload the data set but it includes two groups - normal group and cancer group . Each group has 20 individuals. We would like to find genes associated with cancer. a) How would you test if gene1 is associated with cancer? suggest the hypotheses, test statistic (using two-sample t test), rejection region with sample R code. b) Similarly, please suggest how to find all significant genes which are associated with cancer (and also how to summarize the R outputs and only show the significant genes). Here, we reject the null hypothesis at the level of 5% for each gene (i.e., pvalue 0.05) without Bonferroni correction. c) If you want to control the overall type I error at the level of 5%, how would you perform the test (Bonferroni correction)? Show the significant genes and compare with those found in b). d) Suppose we want to control the false discovery rate (FDR) at the level of 5%, how would you perform the test? report the significant genes and compare with those found in c).
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