The local pooled error test attempts to reduce dependence on the
within-gene estimates in tests for differential expression, by pooling
error estimates within regions of similar intensity. Note that with
the large number of genes there will be genes with low within-gene
error estimates by chance, so that some signal-to-noise ratios will be
large regardless of mean expression intensities and fold-change. The
local pooled error attempts to avert this by combining within-gene
error estimates with those of genes with similar expression intensity.
optional. The member names in the group specified above
name
a prefix name for use when writing output to file
snThresh
S/N ratio threshold to use to define gene detectability
detectSample
percentage of samples detectable above snThresh to
include in LPE test. The default is 50%. If the probe is detected
in 50% or more samples in one of the subgroup, it is considered in
LPE analysis
Value
Dataframe
Details
The LPE test statistic numerator is the difference in medians between
the two experimental conditions. The test statistic denominator is the
combined pooled standard error for the two experimental conditions
obtained by looking up the var.M from each baseOlig.error variance
function. The conversion to p-values is based on the Gaussian
distribution for difference if order statistics (medians). The user
may select both the smoother degrees of freedom (smaller is smoother)
and the trim percent to obtain a variance function to suit particular
issues i.e. variability of genes with low expression intensity.