cghData {fcros}

Example of aCGH "data file" for the fcros package.

Description

This dataset is part of the study performed and published by Sircoulomb et al. 2010, BMC Cancer, 10:539. For our illustration, we used the first 10 patients' data and for only 3 chromosomes: 7, 8 and 9. The complete data are available from the Gene Expression Omnibus website under the accession number GSE17907.

Usage

data(cghData)

Format

A data frame with 33,3613 observations for 10 samples.

Probes:

a text for the unique probe ID

GSM447252:

a numeric vector with log2 change values

GSM447253:

a numeric vector with log2 change values

GSM447254:

a numeric vector with log2 change values

GSM447255:

a numeric vector with log2 change values

GSM447256:

a numeric vector with log2 change values

GSM447257:

a numeric vector with log2 change values

GSM447258:

a numeric vector with log2 change values

GSM447259:

a numeric vector with log2 change values

GSM447260:

a numeric vector with log2 change values

GSM447261:

a numeric vector with log2 change values

Details

This is a subset of a complete dataset obtained using array Comparative Genomic Hybridization technology. Agilent 244K design arrays have been used to monitor breast cancer patients.

References

F Sircoulomb, I Bekhouche, P Finetti, J Adelaide, AB Hamida, J Bonansea, S Raynaud, C Innocenti, E Charafe-Jauffret, C Tarpin, FB Ayed, P Viens, J Jacquemier, F Bertucci, D Birnbaum and M Chaffanet; Genome profiling of ERBB2-amplifief breast cancers. BMC Cancer, 2010, 10:539

Examples

   data(cghData)

   summary(cghData)

   #  perform boxplot of data sample values
   boxplot(cghData[,2:11])