maigesPack (version 1.36.0)

summarizeReplicates: Summarise microarray objects

Description

Function to summarise measures of a maiges class object, both by samples and genes.

Usage

summarizeReplicates(object=NULL, gLabelID="GeneName", sLabelID="Sample", funcS="mean", funcG="mean", rmBad=TRUE, keepEmpty=TRUE)

Arguments

object

object of class maiges.

gLabelID

character string giving the gene label ID to be used to summarise the data by rows.

sLabelID

character string giving the sample label ID to be used to summarise the data by columns.

funcS

character string specifying the function to be applied for sample replicates. Defaults to 'mean'. If NULL, no resume is done for samples.

funcG

character string specifying the function to be applied for genes (spots) replicates. Defaults to 'mean'. If NULL, no resume is done for genes..

rmBad

logical indicating if you want to remove or not bad spots, given by the slot BadSpots in argument object.

keepEmpty

logical indicating if you want to maintain spots with empty information.

Value

This function returns another object of class maiges with replicates summarised to only one observation.

Details

This function takes the object of class maiges and resume the data by spots (rows) and samples (columns).

Examples

## Loading the dataset
data(gastro)

## Summarising the data (maigesNorm class), replicated samples will be
## summarised by mean and genes by median
gastro.summ = summarizeReplicates(gastro.norm, gLabelID="GeneName",
  sLabelID="Sample", funcS="mean", funcG="median",
  keepEmpty=FALSE, rmBad=FALSE)

## To summarise genes by mean and keep the blank spots use
gastro.summ = summarizeReplicates(gastro.norm, gLabelID="GeneName",
  sLabelID="Sample", funcS="mean", funcG="mean",
  keepEmpty=TRUE, rmBad=FALSE)