Agilent normalization (analysis)
- Analysis title
- Agilent normalization
- Institute of Systems Biology
- ru.biosoft.analysis (Common methods of data analysis plug-in)
Normalization of Agilent files based on the functions of the Bioconductor LIMMA package.
Smyth and Speed1 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 log-ratios for one or more two-color spotted microarray experiments so that the log-ratios average to zero within each array or sub-array;
normalizeBetweenArrays- normalizes expression intensities so that the intensities or log-ratios have similar distributions across a set of arrays.
For analyzing single-channel information rather than differential expression based on log-ratios, the data should be normalized using a single channel-normalization technique. Single channel normalization uses further options of the
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 R-project website.
Note: Duplicated identifiers will be modified.
- GK Smyth and TP Speed (2003). Normalization of cDNA microarray data. Methods 31, 265-273.