Normalization methods
The RNA class of interest will be analyzed and compared by the number of normalization methods of choice. Some normalization methods are specific to the properties of certain RNA classes. The user can also decide to analyze data without data normalization or by selecting all normalization methods if the user is uncertain by the method of choice:
| Experimental Bias | Normalization Method | Reference |
|---|---|---|
| Library Size | Counts per Million (CPM) | Dillies, Brief Bioinfor, 2013 |
| Library Size | Total Count (TC) | Dillies, Brief Bioinfor, 2013 |
| Library Size | Upper Quartile (UQ) | Bullard, Bioinfor, 2010 |
| Library Size | Median | Dillies, Brief Bioinfor, 2013 |
| Library Size | Trimmed mean of M values (TMM) | Robinson, Genome Biol, 2010 |
| Library Size | Quantile | Bolstad et al., Bioinfor, 2003 |
| Library Size | Relative log expression (RLE) | Anders, Genome Biol, 2010 |
| Gene Length | Fragment per Kilobase million (FPKM) | Mortazavi, Nat Meth, 2008 |
