Agilent normalization (analysis)
 Analysis title
 Agilent normalization
 Provider
 Institute of Systems Biology
 Class
AgilentNormalization
 Plugin
 ru.biosoft.analysis (Common methods of data analysis plugin)
Agilent Normalization
Normalization of Agilent files based on the functions of the Bioconductor LIMMA package.
Smyth and Speed^{1} give an overview of the normalization techniques implemented in these functions.
Usually data from spotted microarrays will be normalized using the function normalizeWithinArrays
. A minority of data will also be normalized using normalizeBetweenArrays
if diagnostic plots suggest a difference in scale between the arrays:

normalizeWithinArrays
 normalize the expression logratios for one or more twocolor spotted microarray experiments so that the logratios average to zero within each array or subarray; 
normalizeBetweenArrays
 normalizes expression intensities so that the intensities or logratios have similar distributions across a set of arrays.
For analyzing singlechannel information rather than differential expression based on logratios, the data should be normalized using a single channelnormalization technique. Single channel normalization uses further options of the normalizeBetweenArrays
function.
For the detailed description of the LIMMA functions see the LIMMA user�s guide.
Note: Before the Agilent Normalization is started you need to install R and Rserve on your computer. For more information on installing, please visit Rproject website.
Note: Duplicated identifiers will be modified.
References
 GK Smyth and TP Speed (2003). Normalization of cDNA microarray data. Methods 31, 265273.