The genelist node in SciCraft has the
following input arguments:
- model: A fit of a linear model produced by the eBayes
in limma [6]. That is, the ReferenceModel or
ContrastsModel produced by the DiffExp node.
- coefficient: Integer specifying the coefficient number on which
to sort the gene list. Default is set to
.
: Integer specifying the number of genes to include in the
gene list.
- pValueCorrection: Text box specifying which
-value correction
method to use. Has the following six options:
- none (default)
- bonferroni
- holm
- hochberg
- hommel
- fdr
- sortBy: Text box specifying which parameter you are going to
select the
genes on the basis of. Has the following five options:
- B (default)
- A
- M
- P
- T
- resortBy: Text box specifying which parameter you are going sort
the select the
genes by. Has the following four options:
- B
- M (default)
- P
- T
The output arguments from the node are:
- GeneTable: R object containing the following
elements:
- GeneName: Vector containing the names of the top
genes.
- Description: Vector containing the description to the
top
genes.
-
: Vector containing the estimates of the effect or
the contrast, on the log2 scale.
-
: Vector containing the moderated
-statistics.
.value: Vector containing the adjusted
-values
or
-values.
-
: Vector containing the log odds that the genes
are differentially expressed.
Bjørn Kåre Alsberg
2006-04-06