malowess

Smooth microarray data using Lowess method

collapse all in page

    Syntax

    YSmooth = malowess(X,Y)
    YSmooth = malowess(__,Name=Value)

    Description

    YSmooth = malowess(X,Y) smooths scatter data in X and Y using the Lowess smoothing method. The default window size is 5% of the length of X. If Y is a DataMatrix object, then YSmooth is a DataMatrix object with the same properties as Y. Otherwise, YSmooth is a numeric vector.

    example

    YSmooth = malowess(__,Name=Value) specifies additional options with one or more Name=Value arguments.

    Examples

    collapse all

    Open Script

    Read microarray data from a GPR file. Extract data corresponding to cy3 and cy5 emission.

    maStruct = gprread('mouse_a1wt.gpr');
cy5data = magetfield(maStruct,'F635 Median');
cy3data = magetfield(maStruct,'F532 Median');

    Create an intensity versus ratio scatter plot of the cy3 and cy5 data.

    [x,y] = mairplot(cy5data,cy3data);
drawnow

    Smooth the microarray data using the Lowess method and plot the results.

    ysmooth = malowess(x,y);
hold on;
plot(x,ysmooth,'rx')

    Input Arguments

    collapse all

    Scatter data, specified as a DataMatrix object or numeric vector.

    Scatter data, specified as a DataMatrix object or numeric vector.

    Name-Value Arguments

    collapse all

    Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

    Example: malowess(x,y,Robust=true)

    Order of the algorithm, specified as either 1 (linear fit) or 2 (quadratic fit).

    Note that the Curve Fitting Toolbox™ software refers to Lowess smoothing of order 2 as Loess smoothing.

    Example: malowess(X,Y,Order=2)

    Robust fit selection, specified as a numerical or logical 1 (true) or 0 (false).

    The function uses a robust fit when set to true. This option can take a long time to calculate.

    Example: malowess(X,Y,Robust=true)

    Window size, specified as a positive value. The default value is 0.05 (5% of total points in X).

    If the value is less than 1, the window size is set to a fraction of the number of points in the data. If greater than 1, the window size is set to the value specified.

    Example: malowess(X,Y,Span=1.05)

    Version History

    Introduced before R2006a

    See Also

    | | | | | | | |