qualityParameters {arrayMagic}R Documentation

Calculation of quality characteristics for cDNA chip hybridisations

Description

Usage




Arguments

arrayDataObject object of type arrayData; default: missing
exprSetArrayObject object of type exprSetArray; default: missing
spotIdentifier character string, column name used in getSpotAttr(arrayDataObject); the column is used to determine spot replicas; default: "Name"
hybNameColumn character string, column name used in getHybAttr(arrayDataObject); the column is used to extract the names of the hybridisations; if not available the order is taken instead; default: "slideNumber"
identifiersToBeSkipped vector of character strings of spot identifiers to be excluded from calculations
resultFileName character string; results are stored in a file if supplied; default: missing
verbose logical; default TRUE

Details

Value

returns a list of results, i.e. a data frame qualityParameters containing several scores for each hybridisation, a matrix slideDistance and an integer replicateSpots, i.e. the number of spot replicates.
The matrix slideDistance contains a distance measure (similarity) for each pair of slides$_{ij}$, i.e. the median absolute deviation taken over all spots of the difference of the "log-ratios" ("log-ratios": the difference of the expression values in the two channels on the slide).
A brief summary of all parameters given the data frame qualityParameters: width a robust measure of the variance, i.e. the median absolute deviation of the difference of the normalised channels taken over all spots
medianDistance a robust measure for the typical distance (similarity) of one slide with all other slides, i.e. the median of the "distances" between slides (c.f. slideDistance))
correlation of the expression values between the two channels of the slide taken over all spots
meanIntensityCy3 the mean taken over all spots of raw data channel Cy3
meanIntensityCy5 the mean taken over all spots of raw data channel Cy5
meanIntensity mean taken over all spots of raw data of both channels,
spotSimilarityCy3 the standard deviation of all spot replicates for each unique identifier of the normalised channel Cy3 is calculated and the median standard deviation is taken as spotSimilarityCy3; if duplicate spots have been detected, i.e. replicateSpots == 2, the correlation is calculated instead
spotSimilarityCy3 the standard deviation of all spot replicates for each unique identifier of the normalised channel Cy3 is calculated and the median standard deviation is taken as spotSimilarityCy3; if duplicate spots have been detected, i.e. replicateSpots == 2, the correlation is calculated instead
cy3vsAllCy3 and cy5vsAllCy5 the correlation between each channel is measured against the averaged (median) channel over all hybridisations (e.g. a virtual reference)

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

Examples

      spotIdentifierVec <- c("A","A","Blank","B","B","Blank")
      hybNames <- "H1"
      R1 <- N1 <- c(1,1,9,2,2,10)
      R2 <- N2 <- c(2,2,7,4,4,8)
      rawDataIntensities <- array(0, dim=c(6,2,1))
      rawDataIntensities[,1,] <- R1
      rawDataIntensities[,2,] <- R2
      dimnames(rawDataIntensities) <- list(NULL, c("Cy3","Cy5"), NULL)
      spotattr=data.frame(Name=I(spotIdentifierVec))
      hybattr=data.frame(slideNumber=I(hybNames))
      arrayDataObject <- new("arrayData", intensities=rawDataIntensities, hybattr=hybattr, spotattr=spotattr)
      indCy3=1
      indCy5=2
      channels <- matrix( c(indCy3,indCy5), nrow=length(indCy3), byrow=FALSE )
      colnames(channels) <- c("Cy3","Cy5")
      exprSetArrayObject <- new("exprSetArray",         
        exprs=matrix(c(R1,R2), nrow=6, byrow=FALSE), phenoData= 
          new("phenoData", pData=data.frame(matrix(0,nrow=2,ncol=1)),
              varLabels=list(rep("varLabel1",1))), channels=channels)           
      Re1 <- qualityParameters(arrayDataObject=arrayDataObject, exprSetArrayObject=exprSetArrayObject, identifiersToBeSkipped= "Blank")
      stopifnot(all.equal.numeric(as.numeric(Re1$qualityParameters["H1",c("correlation")]),c(1)))
      stopifnot(Re1$replicateSpots==2)
   

        

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