fcrosTtest function

Student t-test for detecting differentially expressed genes

The function uses the basic R t.test() function to perform the Student t-test. It should be used for two biological conditions dataset (microarray, or RNA-seq). The Fold changes, statistics and p-values are returned for each gene in the dataset.

fcrosTtest(xdata, cont, test, log2.opt = 0)

Arguments

• xdata: A table containing a two biological conditions dataset to process for detecting differentially expressed genes. The rownames of xdata are used for the output idnames.
• cont: A vector containing the label names of the control samples: cont = c("cont01", "cont02", ...)
• test: A vector containing the label names of the test samples: test = c("test01", "test02", "test03", ...)
• log2.opt: A scalar equals to 0 or 1. The value 0 (default) means that data in the matrix "xdata" are expressed in a log2 scale: log2.opt = 0

Details

Label names appearing in the parameters "cont" and "test" should match column label names of the data matrix "xdata". It is not necessary to use all column label names of the dataset "xdata".

Returns

• idnames: A vector containing the list of IDs or symbols associated with genes

• FC: The fold changes for the genes in the dataset.

• stat: The Student t-test statistics associated with genes.

• p.value: The Student t-test p-values associated with genes.

Author(s)

Doulaye Dembele

Examples

data(fdata);

   rownames(fdata) <- fdata[,1];

   cont <- c("cont01", "cont07", "cont03", "cont04", "cont08");
   test <- c("test01", "test02", "test08", "test09", "test05");
   log2.opt <- 0;

   # perform fcrosTtest()
   at <- fcrosTtest(fdata, cont, test, log2.opt);
   
   # now select some differentially expressed genes
   id.de  <- matrix(0, 1);
   n <- length(at$FC);
   for (i in 1:n) {
       if ((at$p.value)[i] <= 0.0005) { id.de <- rbind(id.de, i); }
   }

   data.de <- fdata[id.de, ];
   nde <- nrow(data.de);

   # now plot the DE genes
   t <- 1:20;
   plot(t, data.de[1, 2:21], type = "l", col = "blue", xlim = c(1,20),
        ylim = c(0,18), main = "Down- and up-regulated genes");
   for (i in 2:nde) {
       lines(t, data.de[i,2:21], type = "l", col = "blue")
   }