getRLs {GeneExpressionSignature} | R Documentation

## Convert gene expression profiles to a ranked list

### Description

Sorting the micro-array probe-set identifiers according to the differential expression values with respect to the untreated hybridization to obtain a ranked list. Gene-expression profiles in are represented in a nonparametric fashion.

### Usage

    getRLs(control, treatment)

### Arguments

`control` | a matrix, including the vehicle control gene expression profiles corresponding to the treatment gene expression profiles.
`treatment` | a matrix, is composed of gene expression profiles.

### Details

The genes on the array are rank-ordered according to their differential expression relative to the control. First, control and treatment values less than a primary threshold value (quartile) were set to that threshold value. Finally, probe sets were ranked in descending order of d, where d is the ratio of the corresponding treatment-to-control values. For probe sets where d=1, a lower threshold was applied to the original difference values and a new treatment to control ratio (d') calculated. These probe sets were then sub-sorted in descending order of d.

### Value

A matrix is composed of ranked lists, a ranked list represents the corresponding gene expression profiles.

### Examples

    if (require(GEOquery)){
      # treatment gene-expression profiles
      file1 <- system.file(
        "extdata/GSM118720.soft",
        package = "GeneExpressionSignature"
      )
      GSM118720 <- getGEO(filename = file1)

      # control gene-expression profiles
      file2 <- system.file(
        "extdata/GSM118721.soft",
        package = "GeneExpressionSignature"
      )
      GSM118721 <- getGEO(filename = file2)

      # data ranking according to the different expression values
      control <- as.matrix(as.numeric(Table(GSM118721)[, 2]))
      treatment <- as.matrix(as.numeric(Table(GSM118720)[, 2]))
      ranked_list <- getRLs(control, treatment)
    }

[Package GeneExpressionSignature version 1.38.0 Index]