Transform to Relative Expression Levels

This function computes the relative expression profiles of any given gene expression set. The relative expression profile is being computed as follows:

$$f_s = ( e_s - e_min ) / ( e_max - e_min )$$

where $e_min$ and $e_max$ denote the minimum/maximum mean expression level over the developmental stages s. This linear transformation corresponds to a shift by $e_min$ and a subsequent shrinkage by $e_max - e_min$. As a result, the relative expression level $f_s$ of developmental stage s with minimum $e_s$ is 0, the relative expression level $f_s$ of the developmental stage s with maximum $e_s$ is 1, and the relative expression levels $f_s$ of all other stages s range between 0 and 1, accordingly.

Usage

RE(ExpressionMatrix)

Arguments

ExpressionMatrix: a numeric matrix representing a gene expression matrix for which the relative expression profile shall be computed.

Value

a vector containing the relative expression profile of the correspnding data matrix.

References

Domazet-Loso T and Tautz D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (468): 815-818.

Quint M et al. (2012). A transcriptomic hourglass in plant embryogenesis. Nature (490): 98-101.

Author

Hajk-Georg Drost

Examples


# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)

# relative expression profile of PS1 genes
RE(PhyloExpressionSetExample[ which(PhyloExpressionSetExample[ , 1] == 1), 3:9 ])
#>    Zygote  Quadrant  Globular     Heart   Torpedo      Bent    Mature 
#> 0.4816246 0.3145330 0.4638918 0.0000000 0.1706749 0.5688023 1.0000000