lymphoma {vsn} | R Documentation

## Intensity data for 8 cDNA slides with CLL and DLBL samples from the Alizadeh et al. paper in Nature 2000

### Description

8 cDNA chips from Alizadeh lymphoma paper

### Usage

    data(lymphoma)

### Format

`lymphoma` is an `exprSet` 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

       data(lymphoma)
       lymphoma
       pData(lymphoma)

[Package vsn version 1.6.3 Index]