FastBMD accepts a single gene expression data table: a data table containing expression values (i.e. gene/probe intensities from microarray, counts from RNAseq saved as a tab delimited text file (.txt) with rows for features (genes/probes) and columns for samples. The tab delimited file can be generated from any spreadsheet program.
Here is a good tutorial on how to generate tab delimited text files from the Excel Spreadsheet program. When you open your data using any text editor (for example, WordPad), it should look like the following:
- Sample name, one class label (one missing value)
#NAME Sample1 Sample2 Sample3 Sample4 Sampl5 Sampl6 Sample7 Sample8 #CLASS 0 0 0.1 0.1 1.0 1.0 10.0 10.0 Gene1 -3.06 -2.25 -1.15 -6.64 0.4 1.08 1.22 1.02 Gene2 -1.36 -0.67 -0.17 -0.97 -2.32 -5.06 0.28 1.32 Gene3 1.61 -0.27 0.71 -0.62 0.14 0.11 0.98 Gene4 0.93 1.29 -0.23 -0.74 -2 -1.25 1.07 1.27
- Sample name, two class labels (cancer and sex)
#NAME Sample1 Sample2 Sample3 Sample4 Sampl5 Sampl6 Sample7 Sample8 #CLASS:DOSE 0 0 0.1 0.1 1.0 1.0 10.0 10.0 #CLASS:SEX F F M M F M F M Gene1 -3.06 -2.25 -1.15 -6.64 0.4 1.08 1.22 1.02 Gene2 -1.36 -0.67 -0.17 -0.97 -2.32 -5.06 0.28 1.32 Gene3 1.61 -0.27 0.71 -0.62 0.14 0.11 0.98 Gene4 0.93 1.29 -0.23 -0.74 -2 -1.25 1.07 1.27