8 cDNA chips from Alizadeh lymphoma paper
lymphoma is an
containing the data from 8 chips
from the lymphoma data set by Alizadeh et al. (see references). Each
chip represents two samples: on color channel 1 (CH1, Cy3, green) the
common reference sample, and on color channel 2 (CH2, Cy5, red) the
various disease samples. See
pData(lymphoma). The 9216x16
exprs(lymphoma) contains the background-subtracted spot
intensities (CH1I-CH1B and CH2I-CH2B, respectively).
The chip intensity files were downloaded from the Stanford microarray database. Starting from the link below, this was done by following the links Published Data -> Alizadeh AA, et al. (2000) Nature 403(6769):503-11 -> Data in SMD -> Display Data, and selecting the following 8 slides:
Then, the script
makedata.R from the
of this package was run to generate the R data object.
A. Alizadeh et al., Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403(6769):503-11, Feb 3, 2000.
1 2 3
Loading required package: Biobase 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, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Warning message: In read.dcf(con) : URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name' ExpressionSet (storageMode: lockedEnvironment) assayData: 9216 features, 16 samples element names: exprs protocolData: none phenoData sampleNames: lc7b047.reference lc7b047.CLL-13 ... lc7b058.DLCL-0023 (16 total) varLabels: name sample dye varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: name sample dye lc7b047.reference lc7b047 reference Cy3 lc7b047.CLL-13 lc7b047 CLL-13 Cy5 lc7b048.reference lc7b048 reference Cy3 lc7b048.CLL-13 lc7b048 CLL-13 Cy5 lc7b069.reference lc7b069 reference Cy3 lc7b069.CLL-52 lc7b069 CLL-52 Cy5 lc7b070.reference lc7b070 reference Cy3 lc7b070.CLL-39 lc7b070 CLL-39 Cy5 lc7b019.reference lc7b019 reference Cy3 lc7b019.DLCL-0032 lc7b019 DLCL-0032 Cy5 lc7b056.reference lc7b056 reference Cy3 lc7b056.DLCL-0024 lc7b056 DLCL-0024 Cy5 lc7b057.reference lc7b057 reference Cy3 lc7b057.DLCL-0029 lc7b057 DLCL-0029 Cy5 lc7b058.reference lc7b058 reference Cy3 lc7b058.DLCL-0023 lc7b058 DLCL-0023 Cy5
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