Normalize Agilent experiment and control (analysis)
- Analysis title
Normalize Agilent experiment and control
- Provider
- geneXplain GmbH
- Class
AgilentNormalizeAndSplit- Plugin
- com.genexplain.analyses (geneXplain analyses)
Description
This procedure takes Agilent files as input and returns normalized data. Normalization is carried out using methods in the Bioconductor LIMMA package. Individual CEL files are assigned to either 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.
Parameters:
- Experiment files – Files with experimental data
- Control files – Control files
- Dual channel – Dual channel Agilent microarray
- Reverse channels (expert) – Flag to show if red channel should be considered as experiment and green channel as control
- Result logarithm base – Logarithm base of result
- Output table test data – Output table with test data
- Output table control data – Output table with control data
