SpikeIn: SpikeIn Experiment Data: ProbeSet Example

In affy: Methods for Affymetrix Oligonucleotide Arrays

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 E. coli), CreX-5, CreX-3 (phage P1), and DapX-5, DapX-M, DapX-3 (B. subtilis) The cRNA were chosen to match the target sequence for each of the Affymetrix control probe sets. For example, for DapX (a 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 micro-liters 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

affy documentation built on Nov. 8, 2020, 8:18 p.m.