Agilent normalization (analysis)

Analysis title

Agilent normalization

Provider

Institute of Systems Biology

Agilent Normalization

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 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 R-project website.

Note: Duplicated identifiers will be modified.

References

1. GK Smyth and TP Speed (2003). Normalization of cDNA microarray data. Methods 31, 265-273.