SpikeIn: SpikeIn Experiment Data: ProbeSet Example
Description
This ProbeSet represents part of SpikeIn
experiment data set.
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