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.
Formal class 'ExpressionSet' [package "Biobase"] with 7 slots.
A matrix (1000 rows x 31 columns) containing the gene expression data (RMA normalized microarray data).
GEO database ID: GSE65823
GATExplorer CDF genemappers:
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.
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data(ALCLdata) ## list objects included ls() #  "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)) #  1000 31 # density plot of RMA gene values from all dataset plot(density(assay(ALCL)))
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