The condition-specific detection function

Description

SpeCond performs a full condition-specific detection from an expression matrix

Usage

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SpeCond(expressionMatrix, param.detection = NULL, 
multitest.correction.method = "BY", prefix.file = "A",
print.hist.pv = FALSE, fit1 = NULL, fit2 = NULL, 
specificOutlierStep1 = NULL, condition.factor=NULL, 
condition.method=c("mean","max"))

Arguments

expressionMatrix

an ExpressionSet object or a matrix of expression values (in log2); columns are the conditions, rows are genes (or probe sets)

param.detection

the parameter matrix for the detection must contain the values for "lambda", "beta", "per", "md", "mlk" ,"rsd' and "pv" for the two steps of the procedure. Can be obtained by getDefaultParameter or createParameterMatrix

multitest.correction.method

the multitest correction method. The default is "BY", for the possible values see p.adjust

prefix.file

a prefix added to the histogram file (if produced). It will be used to link to the result html pages generated by other functions using the result object of this function (if no other prefix value is implemented). The default is "A". It is useful to change the prefix when you perform a new analysis with different parameters as you may want to compare the results

print.hist.pv

a logical (TRUE/FALSE) value indicating whether a histogram of (non-adjusted) p-values is to be printed; the default is FALSE

Optional parameters:

fit1

the result of fitPrior containing the parameter of the mixture normal model of the expression data. If NULL fitPrior function will be called

fit2

the result of fitNoPriorWithExclusion containing the parameter of the mixture normal model of the expression data ignoring the outliers detected in the first step of the procedure. If NULL, fitNoPriorWithExclusion function will be called

specificOutlierStep1

the list of outliers detected by the first step procedure, result of the getSpecificOtuliersStep1 function. If NULL, getSpecifcOutliersSpep1 will be called

condition.factor

this argument can be used if expressionMatrix is an ExpressionSet object; a factor object of length equal to the number of columns (samples) of the ExpressionSet object specifying which sample(s) belong to which condition (condition.factor levels); can be extracted from the phenoData

condition.method

this argument can be used if expressionMatrix is an ExpressionSet object; the method (mean or max) to summarise the samples by conditions (defined by the condition.factor vector)

Details

SpeCond uses the Mclust function to obtain the mixture of normal distributions uses by the detection procedure.

If expressionMatrix is an ExpressionSet object it is necessary to obtain an expression value matrix. This is obtain by the getMatrixFromExpressionSet function. This take into consideration if condition.factor is not NULL the transformation of the expression values for the several samples of each condition to one expression values for each condition for each gene.

If print.hist.pv is TRUE the histogramme of the non-adjusted p-values is plotted. It is a way to check the normal distribution fitting. If the histogramme is relatively flat the normal distribution(s) fits properly the data.

Value

An object of class sp_list

prefix.file

the prefix used for this analysis. It will be used by default in the function getFullHtmlSpeCondResult and getGeneHtmlPage

fit1

the fitting parameters used by the detection in the first step of the procedure: the result of the fitPrior function called internally or the same as the fit1 argument if not NULL

fit2

the fitting parameters used by the detection in the second step of the procedure: the result of the fitNoPriorWithExclusion function called internally or the same as the fit2 argument if not NULL

specificOutliersStep1

the condition(s) for which the expression value of the gene is detected as outlier in the first step of the procedure. If NULL, no expression value has been detected in the first step. The second fitting ignores these expression values

specificResult

a list of 7 attributes containing al the specific results. This object result of getSpecificResult

Author(s)

Florence Cavalli, florence@ebi.ac.uk

References

C.Fraley and A. E. Raftery, Model-based clustering, discriminant analysis, and density estimation, Journal of the American Statistical Association, Vol. 97, pages 611-631 (2002).

C. Fraley and A. E. Raftery, MCLUST Version 3 for R: Normal Mixture Modeling and Model-based Clustering, Technical Report No. 504, Department of Statistics, University of Washington, September 2006.

See Also

Mclust, fitPrior, fitNoPriorwithExclusion, getSpecificOutliersStep1, getSpecificResult

Examples

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library(SpeCond)
data(expressionSpeCondExample)
dim(expressionSpeCondExample)
##Perform the condition specific detection analysis with SpeCond()
generalResult=SpeCond(expressionSpeCondExample, param.detection=NULL, 
multitest.correction.method="BY", prefix.file="E", print.hist.pv=TRUE, 
fit1=NULL, fit2=NULL, specificOutlierStep1=NULL)