GSload.int {GeneSpring}R Documentation

Read GeneSpring Experiment Interpretation from file

Description

A GeneSpring Experiment Interpretation is read in, usually from a file, but a connection object (like stdin()) can also be passed. The return value can either be an object of class GSint or BioConductor exprSet representing the Experiment Interpretation from GeneSpring.

Usage

gs.int <- GSload.int(filename = "GS_R_in.txt")
expr.set <- GSload.intBC(filename = "GS_R_in.txt", what = "nor")

Arguments

filename Name of the file containing the GeneSpring Experiment Interpretation. Can also be a connection object.
what For GSload.intBC() only. Indicates what data from the GeneSpring Experiment Interpretation should be used. Valid values for what can be nor and raw, representing Normalized or Raw expression values. The Control values cannot be used.

Details

A GeneSpring Experiment INTERPRETATION is quite distinct from a GeneSpring Experiment. See GSload.exp() for more information on GeneSpring Experiments.

A GeneSpring Experiment Interpretation can consist of a maximum of three sets of six (eighteen total) columns for each condition; The sets can be the Normalized, Raw and Control sets and each set can consists of the Average, Min, Max, Standard error, Standard Deviation and Number of samples per condition. The GSint class will be populated based on the names of the columns. The column names can be any of the following:

x.AVERAGE, x.MIN, x.MAX, x.STDERR, x.STDDEV, x.N

Where x can be either N, C or R, representing Normalized, Control and Raw data If there is more than one conditions, each consecutive set is numerbed by adding a number to the end of the name The first column does not have a number and the second will start numbering at 1

If there is more than one type (i.e if there is both Normalized and Raw data), Each value type (AVERAGE, MIN, STDEV etc) is listed first for each data type

Examples:

N.AVERAGE, R.AVERAGE, N.MIN, R.MIN, N.AVERAGE.1, R.AVERAGE.1, N.MIN.1 etc.

Since teh GeneSpring user can determine what data to send to the external program, it is up to the R programmer to determine which columns contains what type of data.

Value

The return value depends on which fucntion was called. The GSload.int function returns a object of class GSint. The GSload.intBC function returns a BioConductor object of class exprSet. See the documentation on GSint and exprSet for more information.

Note

This and any other functions in the GeneSpring package are only useful, when using Agilent Technologies Gene Expression software GeneSpring.

Author(s)

Thon de Boer, Agilent Technologies, Santa Clara, CA, USA thon_deboer@agilent.com

References

For more information on using GeneSpring with R see http://www.chem.agilent.com/scripts/generic.asp?lpage=34733

See Also

GSload.exp, GSsave.exp GSint2BC, BC2GSint

Examples



[Package GeneSpring version 2.4.0 Index]