summarizeReplicates: Summarise microarray objects

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

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.

Details

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

Value

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

Author(s)

Gustavo H. Esteves <[e-mail]>

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)

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.