The DiffExp node in SciCraft has the
following input arguments:
- bioreplica: Vector containing the variable bioreplica information.
- dye.swapped: Vector specifying if variable dye has been
swapped.
- filename: Vector containing the variable filename(s)
- from.bio.matter: Vector containing the variable
from.bio.matter information
- MA: R object containing the normalised microarray data. (Produced by
affy.tools, NormBetweenArrays and NormWithinArray)
- physical.array: Vector containing the variable physical
arrays information
- to.bio.matter: Vector containing the variable
to.bio.matter information
- ReferenceMaterial: String specifying the reference material
used.
- Merges: Text box specifying if a merging should be
performed of replicates should be performed. Has the following two options:
- No Merging (default)
- Merge Replicates
- Nduplicates: Integer specifying the number of duplicate spots
for each gene on each array. Default equal to 1.
The output arguments from the node are:
- Biomaterials: Vector of Strings specifying which
biomaterials that have been analysed.
- Contrasts: R object specifying which contrasts
have been determined.
- ContrastsModel: R object containing the
following elements for the contrast(s):
- t: Numeric vector or matrix of penalised
-statistics.
- p.value: Numeric vector of
values corresponding
to the
-statistics.
- s2.prior: Estimated prior value for
.
- df.prior: Degrees of freedom associated with s2.prior.
- s2.post: Vector giving the posterior values for
.
- lods: Numeric vector or matrix giving the log-odds of
differential expression.
- var.prior: Estimated prior value for the variance of the
log2-fold-change for differentially expressed gene
- F: Numeric vector of
-statistics for testing all
contrast simultaneously equal to zero
- F.p.value: Numeric vector giving
-values corresponding to F
- ReferenceModel: R object containing the
following elements for the reference(s):
- t: Numeric vector or matrix of penalised
-statistics.
- p.value: Numeric vector of
values corresponding
to the
-statistics.
- s2.prior: Estimated prior value for
.
- df.prior: Degrees of freedom associated with s2.prior.
- s2.post: Vector giving the posterior values for
.
- lods: Numeric vector or matrix giving the log-odds of
differential expression.
- var.prior: Estimated prior value for the variance of the
log2-fold-change for differentially expressed gene
- F: Numeric vector of
-statistics for testing all
contrast simultaneously equal to zero
- F.p.value: Numeric vector giving
-values corresponding to F
Bjørn Kåre Alsberg
2006-04-06