ALCLdata {deco} | R Documentation

## Subset of microarray gene expression data from Anaplastic Large Cell Leukemia disease.

### Description

RMA normalized microarray gene expression data from clinical samples of Anaplastic Large Cell Leukemia (ALCL) patients. ALCL subtypes ALK+ (n=11) and ALK- (n=20). Corresponding to GSE65823 (GEO database ID) on Affymetrix HGU133Plus2.0 platform mapped to ENSEMBL genes with genemapperhgu133plus2cdf CDF package from GATEexplorer website. RMA (Robust Multi-Array Average) normalization of microarrays and filtering of genes were applied (from 20172 genes to 1000 genes). Used as example of group-VS-group (binary) comparison with outlier behavior within ALK- samples.

### Usage

    data(ALCLdata)

### Format

Formal class 'ExpressionSet' [package "Biobase"] with 7 slots.

### Value

A matrix (1000 rows x 31 columns) containing the gene expression data (RMA normalized microarray data).

### Source

GEO database ID: GSE65823

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65823

GATExplorer CDF genemappers:

https://doi.org/10.1186/1471-2105-11-221

### References

Scarfo, Irene et al. Identification of a new subclass of ALK negative ALCL expressing aberrant levels of ERBB4 transcripts. Blood (2015). http://dx.doi.org/10.1182/blood-2014-12-614503.

### Examples

    data(ALCLdata)

    ## list objects included
    ls()
    # [1] "ALCLdata"        "sub.ma.3r.1K"    "deco.results.ma"

    # phenodata of each sample
    head(colData(ALCL))

    # classes vector
    classes.ALCL <- colData(ALCL)[,"Alk.positivity"]
    names(classes.ALCL) <- colnames(ALCL)

    # gene expression matrix with 1000 ENSEMBL genes (mapped using GATExplorer genemappers)
    # and 31 samples (11 ALK+ and 20 ALK-)
    dim(assay(ALCL))
    # [1] 1000    31

    # density plot of RMA gene values from all dataset
    plot(density(assay(ALCL)))

[Package deco version 1.8.0 Index]