fom: Figure of Merit

In maanova: Tools for analyzing Micro Array experiments

Description

K-means clustering needs a given number of groups, which is difficult to guess in most of the cases. This function calculates the Figure of Merit values for different number of groups and generates the FOM plot (FOM value versus number of groups). Lower FOM value means better grouping. User can decide the number of groups in kmeans cluster based on that result.

Usage

fom(anovaobj, idx.gene, term, ngroups)

Arguments

anovaobj	An object of class maanova.
idx.gene	The index of genes to be clustered.
term	The factor (in formula) used in clustering. The expression level for this term will be used in clustering. This term has to correspond to the gene list, e.g, idx.gene in this function. The gene list should be the significant hits in testing this term.
ngroups	The number of groups for K-means cluster. This could be a vector or an integer.

Value

A vector of FOM values for the given number of groups

Author(s)

Hao Wu

References

Yeung, K.Y., D.R. Haynor, and W.L.Ruzzo (2001). Validating clustering for gene expression data. Bioinformatics, 17:309-318.

See Also

macluster, consensus, kmeans

Examples

# load in data
data(abf1)
# fit the anova model
## Not run: 
fit.fix = fitmaanova(abf1,formula = ~Strain)
# test Strain effect 
test.fix = matest(abf1, fit.fix, term="Strain",n.perm= 1000)
# pick significant genes - pick the genes selected by Fs test
idx <- volcano(test.fix)$idx.Fs
# generate FOM
m <- fom(fit.fix, idx, "Strain", 10)
## End(Not run)

Example output

Attaching package: 'maanova'

The following object is masked from 'package:base':

    norm

Warning message:
In any(parsed.formula$random) :
  coercing argument of type 'double' to logical
Doing F-test on observed data ...
Doing permutation. This may take a long time ... 
Finish permutation #  100 
Finish permutation #  200 
Finish permutation #  300 
Finish permutation #  400 
Finish permutation #  500 
Finish permutation #  600 
Finish permutation #  700 
Finish permutation #  800 
Finish permutation #  900 
Finish permutation #  1000 
There were 50 or more warnings (use warnings() to see the first 50)

maanova documentation built on Nov. 8, 2020, 8:21 p.m.