The data file contains gene expression data of 62 samples (40 tumor samples, 22 normal samples) from colon-cancer patients analyzed with an Affymetrix oligonucleotide Hum6000 array.
Usage
data(colon)Format
A list of 2 variables:
- X
A 62-by-2000 matrix that records the gene expression data. Used as design matrix.
- y
A binary vector of length 62 recording the sample status: 1 = tumor; 0 = normal. Used as response vector.
Source
The raw data can be found on Bioconductor: https://bioconductor.org/packages/release/data/experiment/html/colonCA.html.
References
Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, and Levine AJ (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. 96: 6745–6750 doi:10.1073/pnas.96.12.6745
Examples
data(colon)
X <- colon$X
y <- colon$y
str(X)
#> num [1:62, 1:2000] 8589 9164 3826 6246 3230 ...
#> - attr(*, "dimnames")=List of 2
#> ..$ : chr [1:62] "t" "n" "t" "n" ...
#> ..$ : chr [1:2000] "Hsa.3004" "Hsa.13491" "Hsa.13491.1" "Hsa.37254" ...
dim(X)
#> [1] 62 2000
X.bm <- as.big.matrix(X, backingfile = "") # convert to big.matrix object
str(X.bm)
#> Formal class 'big.matrix' [package "bigmemory"] with 1 slot
#> ..@ address:<pointer: 0x5622d4db9c70>
dim(X.bm)
#> [1] 62 2000