MantisBT - Visomics | |||||
| View Issue Details | |||||
| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0012828 | Visomics | [All Projects] General | public | 2012-01-06 15:43 | 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 | 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 | ||||
| Steps To Reproduce | |||||
| 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 [^] | ||||
| Tags | No tags attached. | ||||
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| 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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