createData {maanova} | R Documentation

## Calculate and create a data object for Micro Array experiment

### Description

This is the function to create a `madata` object based on the given `rawdata` and some parameters.

### Usage

    createData(rawdata, n.rep=1, avgreps=0, log.trans=TRUE)

### Arguments

`rawdata` | An object of class `rawdata`, which should be the result from `read.madata`.
`n.rep` | An integer to represent the number of replicates.
`avgreps` | An integer to indicate whether to average the replicates or not. 0 means no average; 1 means to take the mean of the replicates; 2 means to take the median of the replicates.
`log.trans` | A logical value to indicate whether to take log2 transformation on the raw data or not. It is TRUE by default. But in the case that your data is pre-transformed, you need to set it to FALSE. If this is TRUE, `TransformMethod` field will be set to "log2".

### Details

The data integrity is checked before making the object. The number of rows for the data must be consistent with the number of replicates; the number of columns for the data must be consistent with the number of dyes, etc.

Users have the option to collapse the replicated spots. Collapsing will be done by taking mean or median of the intensity values for the replicated spots. This function assumes the input data is on raw scale. So if your data is pre-transformed and on a log2 based, collapsing could be wrong. Also note that once the replicated spots are collapsed, you will lose the grid location and spatial loess ("rlowess" option in `transform.madata` will be unapplicable for it.

### Value

An object of class `madata`, which is a list of following components:

`n.gene` | Total number of genes in the experiment.
`n.rep` | Number of replicates in the experiment.
`n.spot` | Number of spots for each gene.
`data` | data field. It is either the log2 transformed rawdata (if log.trans=TRUE), or just the rawdata (if log.trans=FALSE).
`Others` | All other fields in the input object of class `rawdata`.

### Author(s)

Hao Wu hao@jax.org

### Examples

    #################
    # 2-dye arrays
    #################
    data(paigen)
    # create data object with replicate
    data2 <- createData(paigen.raw, n.rep=2)
    # summarize the data object
    summary(data2)
    # create data with averaging of replicates
    data1 <- createData(paigen.raw, n.rep=2, avgreps=1)
    summary(data1)

    ####################################################################
    # affy array - data is pre-transformed so log2 is skipped
    ####################################################################
    data(abf1)
    abf1 <- createData(abf1.raw, n.rep=1, log.trans=FALSE)
    summary(abf1)

[Package maanova version 1.0.0 Index]