CoCalc running Bioconductor's puma & affy

calculateLimma {puma}

R Documentation

Calculate differential expression between conditions using limma

Description

Runs a default analysis using the limma package. Automatically creates design and contrast matrices if not specified. This function is useful for comparing limma results with those of other differential expression (DE) methods such as pumaDE.

Usage

calculateLimma(
	eset
,	design.matrix = createDesignMatrix(eset)
,	contrast.matrix = createContrastMatrix(eset)
)

Arguments

eset	An object of class ExpressionSet
design.matrix	A design matrix
contrast.matrix	A contrast matrix

Details

The eset argument must be supplied, and must be a valid ExpressionSet object. Design and contrast matrices can be supplied, but if not, default matrices will be used. These should usually be sufficient for most analyses.

Value

An object of class DEResult.

Author(s)

Richard D. Pearson

See Also

Related methods pumaDE, calculateTtest, calculateFC, createDesignMatrix and createContrastMatrix and class DEResult

Examples

if (require(affydata)) {
	data(Dilution)
	eset_rma <- affy:::rma(Dilution)
	#	Next line used so eset_rma only has information about the liver factor
	#	The scanner factor will thus be ignored, and the two arrays of each level
	#	of the liver factor will be treated as replicates
	pData(eset_rma) <- pData(eset_rma)[,1, drop=FALSE]
	limmaRes <- calculateLimma(eset_rma)
	topGeneIDs(limmaRes,numberOfGenes=6)
	plotErrorBars(eset_rma, topGenes(limmaRes))
}

---

1. 'AFFX-DapX-M_at'
2. '34103_at'
3. '31642_at'
4. 'AFFX-M27830_5_at'
5. '32934_i_at'
6. 'AFFX-HUMRGE/M10098_M_at'

plotDensity {affy}

R Documentation

Plot Densities

Description

Plots the non-parametric density estimates using values contained in the columns of a matrix.

Usage

plotDensity(mat, ylab = "density", xlab="x", type="l", col=1:6,
            na.rm = TRUE, ...)

plotDensity.AffyBatch(x, col = 1:6, log = TRUE,
                      which=c("pm","mm","both"),
                      ylab = "density",
                      xlab = NULL, ...)

Arguments

mat	a matrix containing the values to make densities in the columns.
x	an object of class AffyBatch.
log	logical value. If TRUE the log of the intensities in the AffyBatch are plotted.
which	should a histogram of the PMs, MMs, or both be made?
col	the colors to use for the different arrays.
ylab	a title for the y axis.
xlab	a title for the x axis.
type	type for the plot.
na.rm	handling of NA values.
...	graphical parameters can be given as arguments to plot.

Details

The list returned can be convenient for plotting large input matrices with different colors/line types schemes (the computation of the densities can take some time).

To match other functions in base R, this function should probably be called matdensity, as it is sharing similarities with matplot and matlines.

Value

It returns invisibly a list of two matrices ‘x’ and ‘y’.

Author(s)

Ben Bolstad and Laurent Gautier

Examples

if (require(affydata)) {
  data(Dilution)
  plotDensity(exprs(Dilution), log="x")
}

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