normScaleLimma {maigesPack} | R Documentation |
This function loads a maigesRaw
or maiges
object and scale adjust (normalise between arrays) the data using
functions from limma package.
normScaleLimma(obj=NULL, ...)
obj |
object of type maigesRaw or
maiges to be normalised. |
... |
additional parameters for function
normalizeBetweenArrays . |
This function for scale adjustment is entirely based on function
normalizeBetweenArrays
from
limma package. See the help page for this function to see how
to set the parameters. Pay attention to the 'vsn' method of scale
adjustment, that must be used alone.
This function returns a maiges
object.
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
normalizeBetweenArrays
from limma package.
## Loading the dataset data(gastro) ## Doing the scale adjustment from median-absolute-value method (from ## limma) gastro.norm = normScaleLimma(gastro.norm, method="scale") boxplot(gastro.norm) ## To see the efect of adjustment ## To do VSN scale adjustment (from vsn package) use the command. Be ## carefull that this method adjust the variance along A values and not ## between chips!! gastro.norm = normScaleLimma(gastro.raw2, method="vsn") boxplot(gastro.norm) ## See the effect