SpikeIn {affy} | R Documentation

## SpikeIn Experiment Data: ProbeSet Example

### Description

This `ProbeSet` represents part of SpikeIn experiment data set.

### Usage

    data(SpikeIn)

### Format

`SpikeIn` is `ProbeSet` containing the $PM$ and $MM$ intensities for a gene spiked in at different concentrations (given in the vector `colnames(pm(SpikeIn))`) in 12 different arrays.

### Source

This comes from an experiments where 11 different cRNA fragments have been added to the hybridization mixture of the GeneChip arrays at different pM concentrations. The 11 control cRNAs were BioB-5, BioB-M, BioB-3, BioC-5, BioC-3, BioDn-5 (all {it E. coli}), CreX-5, CreX-3 (phage P1), and DapX-5, DapX-M, DapX-3 ({it B. subtilis}) The cRNA were chosen to match the target sequence for each of the Affymetrix control probe sets. For example, for DapX (a {it B. subtilis} gene), the 5', middle and 3' target sequences (identified by DapX-5, DapX-M, DapX-3) were each synthesized separately and spiked-in at a specific concentration. Thus, for example, DapX-3 target sequence may be added to the total hybridization solution of 200 $μ$l to give a final concentration of 0.5 pM.

For this example we have the $PM$ and $MM$ for BioB-5 obtained from the arrays where it was spiked in at 0.0, 0.5, 0.75, 1, 1.5, 2, 3, 5, 12.5, 25, 50, and 150 pM.

For more information see Irizarry, R.A., et al. (2001) http://biosun01.biostat.jhsph.edu/~ririzarr/papers/index.html

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