Transformation

Description

Performs transformation of the dataMatrix intensity values aimed at stabilizing variance.
For mass spectrometry data, where multiplicative noise has been reported, logarithm transformation can be useful to make the peak intensity variance independent of the intensity mean (see for example Veselkov et al, 2011).
For the logarithm transformations, log(1+X) is used (to avoid returning -Inf for 0 values); NA values remain unchanged

Veselkov et al (2011). Optimized Preprocessing of Ultra-Performance Liquid Chromatography/Mass Spectrometry Urinary Metabolic Profiles for Improved Information Recovery. Analytical Chemistry, 83:5864-5872.

Workflow position

In the workflow example below, the intensities are first transformed, before the signal drift and batch-effects are corrected; finally, the data quality is evaluated numerically and visually.

Input files

Parameter : num + label	Format
1 : Data matrix file	tabular

Required format for the dataMatrix is described in the HowTo entitled 'Format Data For Postprocessing' available on the main page of Workflow4Metabolomics.org

Parameters

Method | Method to be used for transforming the intensity values of the dataMatrix: | log2 (resp. log10): intensities values are log2 (resp. log10) transformed: log(1+X) is used to avoid generating -Inf for 0 values | in case of negative intensities in the initial dataMatrix, an error is returned | in case of missing (NA) intensities in the initial dataMatrix, these intensities remain set to NA after transformation

Output files

dataMatrix_out.tabular | dataMatrix data file with the transformed intensity values |

information.txt | Text file giving some informations about the computation (eg, number of NA and 0 valuesin the initial dataMatrix) |

Working example

See the W4M00001b_sacurine-complete shared history in the Shared Data/Published Histories menu (https://galaxy.workflow4metabolomics.org/history/list_published)

NEWS

CHANGES IN VERSION 2.2.0

NEW FEATURE

Square root transformation now available

CHANGES IN VERSION 2.0.2

INTERNAL MODIFICATIONS

Creating tests for R code