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

In fcros: A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

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])

fcros documentation built on May 31, 2019, 5:03 p.m.