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.
A list of 2 variables included in colon:
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.
The raw data can be found on Bioconductor: https://bioconductor.org/packages/release/data/experiment/html/colonCA.html.
U. Alon et al. (1999): Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissue probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 96, 6745-6750. https://www.pnas.org/doi/abs/10.1073/pnas.96.12.6745.
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:<externalptr>
dim(X.bm)
#> [1] 62 2000