maNorm {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 six basic location and 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"
.
maNorm(mbatch, norm=c("printTipLoess", "none", "median", "loess", "twoD", "scalePrintTipMAD"), subset=TRUE, span=0.4, Mloc=TRUE, Mscale=TRUE, echo=FALSE, ...)
mbatch |
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 |
Character string specifying the normalization procedures:
|
subset |
A "logical" or "numeric" vector indicating the subset of points used to compute the normalization values. |
span |
The argument span which controls the degree of smoothing in the loess function. |
Mloc |
If TRUE , the location normalization values are stored in the slot maMloc of the object of class "marrayNorm" returned by the function, if FALSE , these values are not retained. |
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. |
... |
Misc arguments |
See maNormMain
for details and also 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 for swirl arrays 2 and 3 mnorm<-maNorm(swirl[,2:3], norm="median", echo=TRUE) # Within-print-tip-group loess location normalization for swirl array 1 mnorm<-maNorm(swirl[,1], norm="p", span=0.45)