decideTests(object,method="separate",adjust.method="BH",p.value=0.05,lfc=0)
MArrayLM
object output from eBayes
or treat
from which the t-statistics may be extracted."separate"
, "global"
, "hierarchical"
, "nestedF"
or any partial string."none"
, "BH"
, "fdr"
(equivalent to "BH"
), "BY"
and "holm"
. See p.adjust
for details.TestResults
.
This is essentially a numeric matrix with elements -1
, 0
or 1
depending on whether each t-statistic is classified as significantly negative, not significant or significantly positive respectively.If lfc>0
then contrasts are judged significant only when the log2-fold change is at least this large in absolute value.
For example, one might choose lfc=log2(1.5)
to restrict to 50% changes or lfc=1
for 2-fold changes.
In this case, contrasts must satisfy both the p-value and the fold-change cutoff to be judged significant.
tstat
correspond to genes and columns to coefficients or contrasts.The setting method="separate"
is equivalent to using topTable
separately for each coefficient in the linear model fit, and will give the same lists of probes if adjust.method
is the same.
method="global"
will treat the entire matrix of t-statistics as a single vector of unrelated tests.
method="hierarchical"
adjusts down genes and then across contrasts.
method="nestedF"
adjusts down genes and then uses classifyTestsF
to classify contrasts as significant or not for the selected genes.
Please see the limma User's Guide for a discussion of the statistical properties of these methods.