mds: MDS gene expression profile
In Pigengene: Infers biological signatures from gene expression data

Description Usage Format Details Value Note Source References See Also Examples

Gene expression profile of 164 myelodysplastic syndromes (MDS) cases from Mills et al. study. The profile was compared with the profile of 202 acute myeloid leukemia (AML) cases and only the 1000 most differentially expressed genes are included.

1	data("mds")

A numeric matrix

The columns and rows are named according to the genes Entrez, and patient IDs, respectively. The original data was produced using Affymetrix Human Genome U133 Plus 2.0 Miccoaray.Mills et al. study is part of the MILE Study (Microarray Innovations In LEukemia) program, and aimed at prediction of AML transformation in MDS.

It is a 164*1000 numeric matrix.

This profile includes data of the 25 chronic myelomonocytic leukemia (CMLL) cases that can have different expression signatures according to Mills et al.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15061

Mills, Ken I., et al. (2009). Microarray-based classifiers and prognosis models identify subgroups with distinct clinical outcomes and high risk of AML transformation of myelodysplastic syndrome. Blood 114.5: 1063-1072.

Pigengene-package, one.step.pigengene, aml, compute.pigengene

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library(pheatmap)
data(mds)
pheatmap(mds[,1:20],show_rownames=FALSE)

Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min