lin: Local intensity-dependent normalisation of two-colour...

In OLIN: Optimized local intensity-dependent normalisation of two-color microarrays

Description

This functions performs local intensity-dependent normalisation (LIN)

Usage

lin(object,X=NA,Y=NA,alpha=0.3,iter=2,scale=TRUE,weights=NA,bg.corr="subtract",...)

Arguments

object	object of class “marrayRaw”
X	matrix with x-coordinates of spots. If X=NA, columns on array are used as proxies for the location in x-direction
Y	matrix with y-coordinates of spots. If Y=NA, rows on array are used as proxies for the location in y-direction
alpha	smooting parameter for local regression
iter	number of iterations in the LIN procedure
scale	scale parameter for smooting in Y-direction of the array in respect to smoothing in X-direcction. If scale=TRUE, standard deviations are used.
weights	matrix of weights for local regression. Rows correspond to the spotted probe sequences, columns to arrays in the batch. These may be derived from the matrix of spot quality weights as defined for “maRaw” objects.
bg.corr	backcorrection method (for “marrayRaw” objects) : “none” or “subtract”(default).
...	Further arguments for locfit function.

Details

LIN is based on the same normalisation scheme as OLIN, but does not incorporate optimisation of model parameters. The function lin can serve for comparison. Alternatively, it can be used to enforce a conservative model fit.

The smoothing parameter alpha controls the neighbourhood size h of local fitting. It specifies the fraction of points that are included in the neighbourhood and, thus, has a value between 0 and 1. Larger alpha values lead to smoother fits.

If the normalisation should be based on set of genes assumed to be not differentially expressed (house-keeping genes), weights can be used for local regression. In this case, all weights should be set to zero except for the house-keeping genes for which weights are set to one. In order to achieve a reliable regression, it is important, however, that there is a sufficient number of house-keeping genes that cover the whole expression range and are spotted accross the whole array.

Value

Object of class “marrayNorm” with normalised logged ratios

Author(s)

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)

References

1. M.Futschik and T.Crompton (2004) Model selection and efficiency testing for normalization of cDNA microarray data, Genome Biology, 5:R60

See Also

maNorm, locfit, olin,oin

Examples

# LOADING DATA
  data(sw)
  data(sw.xy)

# LOCAL INTENSITY-DEPENDENT NORMALISATION 
 norm.lin <- lin(sw,X=sw.xy$X,Y=sw.xy$Y)

# MA-PLOT OF NORMALISATION RESULTS OF FIRST ARRAY
 plot(maA(norm.lin)[,1],maM(norm.lin)[,1],main="LIN")
 
# CORRESPONDING MXY-PLOT
   mxy.plot(maM(norm.lin)[,1],Ngc=maNgc(norm.lin),Ngr=maNgr(norm.lin),
                Nsc=maNsc(norm.lin),Nsr=maNsr(norm.lin),main="LIN")

OLIN documentation built on Nov. 8, 2020, 7:44 p.m.