GSload.exp {GeneSpring} | R Documentation |
A GeneSpring Experiment 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.exp(filename = "GS_R_in.txt") expr.set<-GSload.expBC(filename = "GS_R_in.txt")
filename |
Name of the file containing the GeneSpring Experiment Interpretation. Can also be a connection object. |
A GeneSpring Experiment is quite distinct from a GeneSpring Experiment INTERPRETATION.
See GSload.int
for more information on GeneSpring Experiment Interpretations.
A GeneSpring Experiment consists of the Normalized expression values for each sample and optionally the Control values for that normalized value. The control values for an experiment are the values that are used to create the normalized values by simply dividing the Raw expression value by the Control value. The GeneSpring Normalization routines will calculate the control values for each gene and these values can be used in subsequent analysis.
In a GeneSpring Experiment, each sample or hybridization has its own column (set) of expression values, wheras the expression values for an Experiment INTERPRETATION represent the mean value of the replicate values for that condition.
For example, if there are 4 replicates for samples of time 0, there will be one column of normalized data for time 0 in the Experiment Interpretation, and there will be four columns of average values for each of the replicates, in the GeneSpring Experiment.
The experimental parameters for the experiment, are stored in the header of the file,
with each sample's parameter in columns above the expression values. When control values
are present in the file, the paramter value is simply control
.
The names of the experimental parameters can also indicate whether or not the parameter has any unit indentifier (like hour, mM, etc.) and this will be a suffix of the parameter name in parenthesis. The experimental parameters will also contain an indication wheter or not the values are numeric or not, but the addition of an asterisk character for non-numeric values and the absence of the asterisk for numerical values.
The final character of the parameter name will indicate how the parameter was used in GeneSpring. When the parameter is used as a discontinuous parameter, the character is a ‘C’. When the parareter is used as a color coding paramter, the character is a ‘S’. When the parameter is not used to indicate a group or color coding the character is a ‘R’. When a parameter was used as the continuous parameter, the last character is missing or empty.
When loading experimental parameters from file, the units and indication of use will be discarded.
The return value depends on which fucntion was called.
The GSload.exp
function returns a object of class GSint
.
The GSload.expBC
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 Agilent Technologies Gene Expression software GeneSpring.
Thon de Boer, Agilent Technologies, Santa Clara, CA, USA thon_deboer@agilent.com
For more information on using GeneSpring with R see http://www.chem.agilent.com/scripts/generic.asp?lpage=34733
GSload.int
,
GSsave.exp
,
GSint2BC
,
BC2GSint