
678 Statistics and Data Analysis for Microarrays Using R and Bioconductor
Much like the Affymetrix arrays, the Illumina arr ays also include various
positive and negative controls that should signal if something goes wrong
during the proce ssing pipeline.
Controls for biological specimen: These are housekeeping genes that
should be expressed in all samples.
Controls for sample labeling: These are RNA spikes lysA, pheA,
thrB, trpF. These are spiked into samples immediately before the re-
verse transcription and labeling reactions. Low signals from thes e probes
indicates problems with these reactions. This type of control is optional.
Controls for hybridization: ...