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

In vsn: Variance stabilization and calibration for microarray data

Description

8 cDNA chips from Alizadeh lymphoma paper

Usage

data(lymphoma)

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.

Examples

   data("lymphoma")
   lymphoma
   pData(lymphoma)

vsn documentation built on Nov. 8, 2020, 8:03 p.m.