Chowdary Database

Description

The original authors compared pairs of snap-frozen and RNAlater preservative-suspended tissue from lymph node-negative breast tumors (B) and Dukes' B colon tumors (C). The actual data set, by de Souto et. al (2008), is build with purpose of separating B from C.

Usage

data(chowdary)

Format

Data frame with 183 rows and 104 columns.

Source

Actual source http://algorithmics.molgen.mpg.de/Static/Supplements/CompCancer/Affymetrix/chowdary-2006

Original source http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3726

References

de Souto MCP, Costa IG, de Araujo DSA, Ludermir TB, and Schliep A (2008). Clustering Cancer Gene Expression Data: a Comparative Study. BMC Bioinformatics, 8, 497–511.

Chowdary D, Lathrop J, Skelton J, Curtin K, Briggs T, Zhang Y, Yu J, Wang X, and Mazumder A (2006). Prognostic gene expression signatures can be measured in tissues collected in RNAlater preservative. Journal Molecular Diagnosis, 8, 31–39.

Examples

data(chowdary)

tumor <- as.factor(as.matrix(chowdary[1,]))
x <- as.matrix(chowdary[-1,])
mode(x) <- "numeric"

s <- sample(row.names(x),1)
boxplot( x[s,] ~ tumor , ylab=s)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ICGE)
Loading required package: MASS
Loading required package: cluster
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ICGE/chowdary.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chowdary
> ### Title: Chowdary Database
> ### Aliases: chowdary
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(chowdary)
> 
> tumor <- as.factor(as.matrix(chowdary[1,]))
> x <- as.matrix(chowdary[-1,])
> mode(x) <- "numeric"
> 
> s <- sample(row.names(x),1)
> boxplot( x[s,] ~ tumor , ylab=s)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>