getSpecificOutliersStep1 {SpeCond} | R Documentation

## Detect the condition-specific as outliers in for the first step on the SpeCond procedure

### Description

Perform the first detection step of the SpeCond procedure. Use the fitting of the gene expression value with a mixture of normal distribution results and a set of rules to detect the outliers. It returns the outliers detected as specifically expressed for each gene.

### Usage

    getSpecificOutliersStep1(expressionMatrix, fit1 = NULL,
    param.detection = NULL, multitest.correction.method = "BY",
    prefix.file = NULL, print.hist.pv = FALSE)

### Arguments

`expressionMatrix` | the gene expression matrix (genes * conditions)
`fit1` | the result of `fitPrior` containing the parameter of the mixture normal model of the expression data
`param.detection` | the parameter for the detection, a vector with the names ("per","md","mlk","rsd","pv") or the first row of the matrix obtained by `getDefaultParameter` or `createParameterMatrix`
`multitest.correction.method` | the multitest correction method. The default is "BY", for the possible values see `p.adjust`
`prefix.file` | a prefix added to the generated file. The default is NULL but has to be set. It is useful to change the prefix when you perform a new analysis. As you may want to compare the results with different parameters set.
`print.hist.pv` | to print in a pdf file the (non-adjusted) p-value histogram

### Details

Frist essential method to obtain the matrix of expression value from your ExpressionSet to apply the SpeCond procedure step by step using the following function `fitPrior`, `fitNoPriorwithExclusion`, `getSpecificOutliersStep1`, `getSpecificResult`. The returned matrix will be the expressionMatrix argument of the above function

### Value

A list of size the number of rows (genes) in the expressionMatrix. If the gene has outlier expression, the column number of this outlier is stored, NULL if not.

### Author(s)

Florence Cavalli, florence@ebi.ac.uk

### See Also

`fitPrior`, `SpeCond`, `getSpecificResult`

### Examples

    library(SpeCond)
    data(expressionSpeCondExample)
    ##Perform the SpeCond analysis step by step
    param.detection=getDefaultParameter()
    param.detection

    fit1=fitPrior(expressionSpeCondExample, param.detection=param.detection)

    specificOutlierStep1=getSpecificOutliersStep1(expressionSpeCondExample,
     fit=fit1$fit1, param.detection, multitest.correction.method="BY",
     prefix.file="run1_Step1", print.hist.pv=FALSE)

    ##then use fitNoPriorWithExclusion() and getSpecificResult()

[Package SpeCond version 1.34.0 Index]