data-cancer: Microarray data set for breast cancer

In simone: Statistical Inference for MOdular NEtworks (SIMoNe)

Description

This gene expression data set is freely available, coming from the Hess et al's paper. It concerns one hundred thirty-three patients with stage I–III breast cancer. Patients were treated with chemotherapy prior to surgery. Patient response to the treatment can be classified as either a pathologic complete response (pCR) or residual disease (not-pCR). Hess et al developed and tested a reliable multigene predictor for treatment response on this data set, composed by a set of 26 genes having a high predictive value.

The dataset splits into 2 parts (pCR and not pCR), on which network inference algorithms should be applied independently or in the multitask framework: only individuals from the same classes should be consider as independent and identically distributed.

Usage

data(cancer)

Format

A list named cancer comprising two objects:

expr

a data.frame with 26 columns and 133 rows. The nth row gives the expression levels of the 26 identified genes for the nth patient. The columns are named according to the genes.

status

a factor of size 133 with 2 levels ("pcr" and "not"), describing the status of the patient.

References

K.R. Hess, K. Anderson, W.F. Symmans, V. Valero, N. Ibrahim, J.A. Mejia, D. Booser, R.L. Theriault, U. Buzdar, P.J. Dempsey, R. Rouzier, N. Sneige, J.S. Ross, T. Vidaurre, H.L. Gomez, G.N. Hortobagyi, and L. Pustzai (2006). Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with Paclitaxel and Fluorouracil, Doxorubicin, and Cyclophosphamide in breast cancer, Journal of Clinical Oncology, vol. 24(26), pp. 4236–4244.

Examples

## load the breast cancer data set
data(cancer)
attach(cancer)

## histogram of gene expression levels
par(mfrow=c(1,2))
hist(as.matrix(expr[status == "pcr",]), main="pCR")
hist(as.matrix(expr[status == "not",]), main="not pCR")

## mean of gene expression levels for pCR and not-pCR
colMeans( expr[ which( status=="not"), ] )
colMeans( expr[ which( status=="pcr"), ] )
detach(cancer)

Example output

Loading required package: mixer

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      'simone' package version 1.0-3
      SIMoNe page (http://julien.cremeriefamily.info/simone.html)

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Note that versions >= 1.0-0 are not compatible with versions < 1.0.0. 
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    AMFR    BB_S4    BECNI     BTG3     CA12   CTNND2     E2F3    ERBB4 
6.264445 5.282924 6.101005 5.174457 4.605596 5.169860 5.408653 5.192250 
 FGFRIOP FLJ10916 FLJI2650     GAMT    GFRAI   IGFBP4   JMJD2B  KIA1467 
5.299649 5.894089 5.519410 5.174620 5.003421 6.313948 5.544588 5.697762 
    MAPT  MBTP_SI     MELK    METRN   PDGFRA    RAMPI     RRM2   SCUBE2 
5.675195 4.292732 5.442534 6.006570 5.313062 5.545774 5.910873 6.122673 
  THRAP2   ZNF552 
5.796715 6.029533 
    AMFR    BB_S4    BECNI     BTG3     CA12   CTNND2     E2F3    ERBB4 
5.982409 5.109918 5.934486 5.872426 4.459674 4.984173 5.938230 4.737531 
 FGFRIOP FLJ10916 FLJI2650     GAMT    GFRAI   IGFBP4   JMJD2B  KIA1467 
5.194633 5.694224 5.250766 4.792440 4.143609 5.452067 5.372901 5.362385 
    MAPT  MBTP_SI     MELK    METRN   PDGFRA    RAMPI     RRM2   SCUBE2 
5.086714 3.963868 6.086599 5.276473 5.023985 5.212539 6.332193 4.698166 
  THRAP2   ZNF552 
5.527584 5.773354 

simone documentation built on May 2, 2019, 2:37 a.m.