Description Usage Arguments Details Value Author(s) References See Also Examples
An ExpressionSet
object (Biobase
package) that contains
expression values normalized for use with the Iterative Signature
Algorithm.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## S4 method for signature 'ISAExpressionSet'
featExprs(object)
## S4 method for signature 'ISAExpressionSet'
sampExprs(object)
## S4 method for signature 'ISAExpressionSet'
hasNA(object)
## S4 replacement method for signature 'ISAExpressionSet'
hasNA(object) <- value
## S4 method for signature 'ISAExpressionSet'
prenormalized(object)
## S4 replacement method for signature 'ISAExpressionSet'
prenormalized(object) <- value
|
object |
An |
value |
A logical scalar, new value of the |
An ISAExpressionSet
contains three expression matrices.
In most cases, when then ISAExpressionSet
was produced by the
ISANormalize
function, these are: the original, raw
data, the feature-wise scaled and centered data and the sample-wise
scaled and centered data.
Two additional methods were defined to access the extra matrices:
featExprs
returns the feature-wise standardized data,
sampExprs
the sample-wise standardized one.
The hasNA
function returns TRUE
if NA
or
NaN
values appear in at least one of the expression matrices.
The prenormalized
function returns TRUE
if the data was
prenormalized, see ISANormalize
for details.
featExprs
and sampExprs
both return a matrix.
hasNA
and prenormalized
return a logical vector of
length one.
Gabor Csardi csardi.gabor@gmail.com
Bergmann S, Ihmels J, Barkai N: Iterative signature algorithm for the analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.
ISANormalize
, ExpressionSet
in the Biobase
package.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | library(ALL)
data(ALL)
# Do the normalization
ALL.normed <- ISANormalize(ALL)
class(ALL.normed)
dim(exprs(ALL.normed))
dim(featExprs(ALL.normed))
dim(sampExprs(ALL.normed))
# Check that we indeed have Z-scores
all(abs(apply(featExprs(ALL.normed), 2, mean) ) < 1e-12)
all(abs(1-apply(featExprs(ALL.normed), 2, sd)) < 1e-12)
all(abs(apply(sampExprs(ALL.normed), 1, mean) ) < 1e-12)
all(abs(1-apply(sampExprs(ALL.normed), 1, sd)) < 1e-12)
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