## Normalisation / cDNA

### Description

Normalize cDNA arrays to remove systematic bias.

### Parameters

- Background treatment method (none, subtract, edwards, normexp) [subtract]
- Background offset (0, 50) [0]
- Within array normalization method (none, median, loess) [loess]
- Between array normalization method (none, scale, quantile, vsn) [none]

### Details

There are three background removal methods. Either the bakcground is not removed at all, or it is subtracted form the foregound (spot) intensities. The third possibility is to use Edward's smoothing method for background removal. The fourth method, normexp is found to be superior to other methods, expecially when combined with background offset of 50.

Within array normalization methods offer basic options. Either no normalization is applied, arrays are translated to the same median or a loess smoother is used for removing possible nonlinear (dye) effect from the data.

Between array normalizations are no normalization, translation to the same median and quantile. It is also possible to use variance stabilizing normalization. Please note that during normalization the data is also log2-transformed

### Output

A tab-delimited text file containing gene names, expression estimates and call values ("flags"). This file is suitable for all further analyses.

### References

This tool uses Bioconductor package limma.

For normalization, please cite:

Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray data. Methods 31, 265-273.

For background correction steps, please cite:

Ritchie, M. E., Silver, J., Oshlack, A., Silver, J., Holmes, M., Diyagama, D., Holloway, A., and Smyth, G. K. (2007). A comparison of background correction methods for two-colour microarrays. Bioinformatics.