View source for Normalize Illumina experiment and control (analysis)

==== Description ====
This procedure takes Illumina files as input and returns normalized data. Files with Illumina probe IDs or with Illumina Gene IDs in several different formats can be processed. Normalization of Illumina files is carried out using functions of the Bioconductor LUMI package. Currently, the geneXplain platform can perform normalization for raw Illumina files generated by the BeadStudio and the GenomeStudio.

Individual files need to be assigned to the test condition (experiment, study, treatment) or control condition.

The first step normalizes test and control measurements altogether and calculates normalized signal values. By default, the normalization procedure assumes single-channel data. For proper processing of two-channel data, it is necessary to mark the corresponding checkbox in the input form.

Next, the table comprising both test and control values is split yielding two tables for each experiment group. The resulting tables, "Experiment normalized" and "Control normalized", can be applied in subsequent next workflows, such as Compute differentially expressed genes and Gene set enrichment analysis.

As there is quite a number of different formats of the Illumina raw files, processing of all formats is not guaranteed. If the format you have could not be processed, please kindly let us know and send the example format ([mailto:info@genexplain.com info@genexplain.com]).