ssp2003: SSP2003 classifier for identification of breast cancer...

In genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

Description

List of parameters defining the SSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003).

Usage

data(ssp2003)
data(ssp2003.scale)
data(ssp2003.robust)

Format

List of parameters for SSP2003:

centroids

Gene expression centroids for each subtype.

centroids.map

Mapping for centroids.

method.cor

Method of correlation used to compute distance to the centroids.

method.centroids

Method used to compute the centroids.

std

Method of standardization for gene expressions.

mins

Minimum number of samples within each cluster allowed during the fitting of the model.

Details

Three versions of the model are provided, each of ones differs by the gene expressions standardization method since it has an important impact on the subtype classification:

ssp2003

Use of the official centroids without scaling of the gene expressions.

ssp2003.scale

Use of the official centroids with traditional scaling of the gene expressions (see scale).

ssp2003.robust

Use of the official centroids with robust scaling of the gene expressions (see rescale).

The model ssp2003.robust has been shown to reach the best concordance with the traditional clinical parameters (ER IHC, HER2 IHC/FISH and histological grade). However the use of this model is recommended only when the dataset is representative of a global population of breast cancer patients (no sampling bias, the 5 subtypes should be present).

Source

http://www.pnas.org/content/100/14/8418

References

T. Sorlie and R. Tibshirani and J. Parker and T. Hastie and J. S. Marron and A. Nobel and S. Deng and H. Johnsen and R. Pesich and S. Geister and J. Demeter and C. Perou and P. E. Lonning and P. O. Brown and A. L. Borresen-Dale and D. Botstein (2003) "Repeated Observation of Breast Tumor Subtypes in Independent Gene Expression Data Sets", Proceedings of the National Academy of Sciences, 1(14):8418–8423

Examples

data(ssp2003)
str(ssp2003)
data(ssp2003.robust)
str(ssp2003.robust)

genefu documentation built on Jan. 28, 2021, 2:01 a.m.