#For your boxplot,
#Say you wanna make a boxplot for gene UCA1, you wuold type
goi <- norm.all[rownames(norm.all) == "UCA1" , ]
boxplot(goi)

#or

goi <- melt(norm.all[grepl(x = rownames(norm.all), pattern = "GENEOFINTEREST"), ])
boxplot(goi)




studentT <- function(x, s1, s2){
  x <- as.numeric(x);
  x1 <- x[s1];
  x2 <- x[s2];
  z <- t.test(x1, x2, alternative = "two.sided");
  pval <- z$p.value;
  return(pval);
}

# We're applying the function studentT to our object tmp.all that has in the first 168 lines normal samples and the rest cancer
tmp.all.pval <- apply(tmp.all, 1, studentT, s1 = c(1:168), s2 = c(169:588))