| normScaleMarray {maigesPack} | R Documentation |
This function loads a maigesRaw or maiges
object and scale adjust (normalise between arrays) the data using
functions from marray package.
normScaleMarray(obj=NULL, ...)
obj |
object of type maigesRaw or
maiges to be normalised. |
... |
additional parameters for function
maNormScale. |
This function for scale adjustment is entirely based on function
maNormScale from marray package. See the
help page for this function to see how to set the parameter. Pay
attention to the subset argument that is fixed directly from
the UseSpots and BadSpots from obj object, and
must not be specified in the additional arguments.
The functionality of the scale adjustment function from marray
package was added because it uses an estimator of MAD different from
that one used in limma package. Also, using
maNormScale function it is possible to do print
tip scale adjustment.
This function returns a maiges object.
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
maNormScale from marray package.
## Loading the dataset data(gastro) ## Doing global MAD scale adjustment gastro.norm = normScaleMarray(gastro.norm, norm="globalMAD") boxplot(gastro.norm) ## To see the effect of MAD adjustment ## For print tip MAD use the following command ## Not run: gastro.norm = normScaleMarray(gastro.norm, norm="printTipMAD") ## End(Not run)