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0012828

Visomics

[All Projects] General

public

2012-01-06 15:43

Reporter

Jean-Christophe Fillion-Robin

Assigned To

Jean-Christophe Fillion-Robin

Priority

urgent

Severity

feature

Reproducibility

have not tried

Status

assigned

Resolution

open

Platform

OS Version

Summary

0012828: Normalization algorithms

Description

So far three normalization techniques will be implemented:

Householding
- http://wiki.c2b2.columbia.edu/workbench/index.php/Normalization#Housekeeping_Genes_Normalizer [^]

log2:
- Apply log2 to each values
- http://stat.ethz.ch/R-manual/R-devel/library/base/html/Log.html [^]

Quantile:
  - http://en.wikipedia.org/wiki/Quantile_normalization [^]
  - http://mathworld.wolfram.com/Quantile.html [^]
  - http://stat.ethz.ch/R-manual/R-devel/library/stats/html/quantile.html [^]
  - http://stackoverflow.com/questions/95007/explain-the-quantile-function-in-r [^]
  - http://en.wikipedia.org/wiki/Quantile_normalization [^]
  - Package preprocessCore from bioconductor
     - See http://svitsrv25.epfl.ch/R-doc/library/preprocessCore/html/normalize.quantiles.html [^]
     - http://www.bioconductor.org/packages/2.5/bioc/html/preprocessCore.html [^]

File "Base/voUtils.h" should be created.

Normalization will be done on the table passed as parameter. In case, changes need to be undone. It will be the responsibility of the caller to make a copy of the table before hand.

Suggested API:

namespace voUtils {

void log2Normalization(voTable* table);

void housekeepingNormalization(voTable* table);

void quantileNormalization(voTable* table);

} // end voUtils namespace

Additional Information

Wes> As we discussed during the t-con (March 29th 2011), I think we also need to make this a tabbed menu with the second tab being "Normalize" and a set of checkboxes for normalization options to be used during the import. I think we had 3 so far: Householding, log2 and Quantile.

"In an experimental context, normalizations are used to standardise microarray data to enable differentiation between real (biological) variations in gene expression levels and variations due to the measurement process.

In microarray analysis, normalization refers to the process of identifying and removing the systematic effects, and bringing the data from different microarrays onto a common scale."
Source: http://en.wikipedia.org/wiki/Normalization_%28statistics%29#Applications [^]

Issue History
Date Modified	Username	Field	Change
2012-01-06 15:43	Matthew Bowman	New Issue
2012-01-06 15:43	Matthew Bowman	Assigned To	=> Jean-Christophe Fillion-Robin

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