GSload.int {GeneSpring} | R Documentation |
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.
gs.int <- GSload.int(filename = "GS_R_in.txt") expr.set <- GSload.intBC(filename = "GS_R_in.txt", what = "nor")
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. |
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.
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.
This and any other functions in the GeneSpring package are only useful, when using Silicon Genetics Gene Expression software GeneSpring.
Thon de Boer, Silicon Genetics, Redwood city, CA, USA thon@silicongenetics.com
For more information on using GeneSpring with R see http://www.silicongenetics.com/cgi/SiG.cgi/Support/GeneSpring/GSnotes/R.smf
GSload.exp
,
GSsave.exp
GSint2BC
,
BC2GSint