lymphoma: Intensity data for 8 cDNA slides with CLL and DLBL samples...

Description Usage Format Details Source References See Also Examples

Description

8 cDNA chips from Alizadeh lymphoma paper

Usage

1

Format

lymphoma is an ExpressionSet 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 matrix exprs(lymphoma) contains the background-subtracted spot intensities (CH1I-CH1B and CH2I-CH2B, respectively).

Details

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:

lc7b019
lc7b047
lc7b048
lc7b056
lc7b057
lc7b058
lc7b069
lc7b070

Then, the script makedata.R from the scripts subdirectory of this package was run to generate the R data object.

Source

http://genome-www5.stanford.edu/MicroArray/SMD

References

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.

See Also

vsn

Examples

1
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3

Example output

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

vsn documentation built on May 31, 2017, 11:06 a.m.