## Normalisation / Illumina - lumi pipeline AAI

### Description

Normalize Illumina arrays to remove systematic bias. This versions of the tool is to be used when the Probe_Id column is unavailable in the data file and instead Array_Address_Id is present. For data including the Probe_Id column, please use the "Illumina - lumi pipeline" tool instead.

Array_Address_Id identifiers look like this: 4900685 Probe_Id identifiers look like this: ILMN_2607609

Please note that in order to use the lumi normalization, your raw data must be in one file. The filename must end with ".txt", and you should NOT use the Import tool for bringing the data into Chipster (in the Import files -window change the action to "Import directly").

### Parameters

- Transformation (none, vst, log2) [log2]
- Normalize genes (none, rsn, loess, quantile, vsn) [quantile]
- Chip type (empty, ....) [empty]

### Details

This tool normalizes Illumina BeadSummaryData files.

Note that you have to enter the chiptype.

Within array normalization methods offer basic options: no normalization, robust spline normalization (combines features of loess and quantile normalizations), loess, quantile and variance stabilizing normalization.

### Output

A tab-delimited text file containing gene names and expression estimates. This file is suitable for all further analyses.

### References

This tool uses Bioconductor package lumi. Please cite the article:

Du P, Kibbe WA, Lin SM (2008) lumi: a pipeline for processing Illumina microarray, Bioinformatics, 24, 1547-1548.