removeFlatGenes:
Flags a set of genes which demonstrates little variation across the celltypes or experimental groups of interest.
Description
This function uses a linear model set up in limma to assess the degree of association between celltype and a gene's expression
profile. In this way, we can flag those genes whose profiles show very little change across different celltype groups, or in other words
are "flat".
character string of the variable name which stores the cell-lineages or experimental groups of interest for the samples in the data set
(this string should be one of the column names of pData(myEset)).
contrasts
optional vector of contrasts that specify the comparisons of interest. By default, all comparisons between the differnt groups are generated.
limma.cutoff
numeric specifying the P-value cutoff. Genes with P-values greater than this value are considered "flat" and will be included in the
set of flat genes.
...
additional arguments.
Value
A vector with gene names (as defined in the eset) of those genes with expression profiles that hardly vary across
different celltype or experimental groups.
Details
Flat genes are removed from the analysis after the core attractor pathway modules are first inferred (i.e. the findAttractors step).
References
limma package.
Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, No. 1, Article 3.