maNormScale {marrayNorm} | R Documentation |
This function is a simple wrapper function around the main normalization
function maNormMain
. It allows the user to choose from a
set of two basic scale normalization procedures. The function operates
on an object of class "marrayRaw"
(or possibly
"marrayNorm"
, if normalization is performed in several
steps) and returns an object of class "marrayNorm"
. This
function can be used to conormalize a batch of arrays
(norm="globalMAD"
option).
maNormScale(mbatch, norm=c("globalMAD", "printTipMAD"), subset=TRUE, geo=TRUE, Mscale=TRUE, echo=FALSE)
mbatch |
An object of class "marrayRaw" , containing
intensity data for the batch of arrays to be normalized. An object of class
marrayNorm may also be passed if normalization is performed
in several steps. |
norm |
A character string specifying the normalization
procedures:
|
subset |
A "logical" or "numeric" vector indicating the subset of points used to compute the normalization values. |
geo |
If TRUE , the MAD of each group is divided by the
geometric mean of the MADs across groups (cf. Yang et al. (2002)). This allows observations to
retain their original units. |
Mscale |
If TRUE , the scale normalization values are stored in the slot maMscale of the object of class "marrayNorm" returned by the function, if FALSE , these values are not retained. |
echo |
If TRUE , the index of the array currently being
normalized is printed. |
See maNormMain
for details and more general procedures.
mnorm |
An object of class "marrayNorm" , containing the normalized intensity data. |
Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine.
S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, The Analysis of Gene Expression Data: Methods and Software, Springer, New York.
Y. H. Yang, S. Dudoit, P. Luu, and T. P. Speed (2001). Normalization for cDNA microarray data. In M. L. Bittner, Y. Chen, A. N. Dorsel, and E. R. Dougherty (eds), Microarrays: Optical Technologies and Informatics, Vol. 4266 of Proceedings of SPIE.
Y. H. Yang, S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngai, and T. P. Speed (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research, Vol. 30, No. 4.
# Examples use swirl dataset, for description type ? swirl data(swirl) # Global median normalization followed by global MAD normalization for # only arrays 2 and 3 in the batch swirl mnorm1<-maNorm(swirl[,2:3], norm="m") mnorm2<-maNormScale(mnorm1, norm="g")