Illumina Expression Array System

The Illumina system is a single-color oligo array that uses the random self-assembly of microspheres into ordered microwells. DNA probes are physically attached to multiple microspheres providing data from multiple independent hybridizations that are averaged to produce signal values. Key features are:

• Probes are single 50-mer oligos
• Samples are labeled Cy3, which is then detected as signal
• For more information, see this file: IlluminaWholeGenome.pdf

Illumina currently offers whole genome microarrays for Human, Mouse, and Rat. The Human-6 Expression BeadChip contains six arrays on a single BeadChip, each with >46,000 probes derived from human genes in the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) and UniGene databases. The HumanRef-8 Expression BeadChip contains eight arrays of > 24,000 probes derived from the RefSeq database

Illumina Software

Raw data from Illumina arrays is processed and normalized in the BeadStudio software from Illumina - data can then be exported in a flexible format that can be read by nearly any statistical or microarray package.

Illumina Data

Data is exported from the BeadStudio as a tab-delimited text file which can be easily loaded into your favorite analysis package (or Excel). If you receive unprocessed data you will only have AVG_Signal and Detection_Pval. If you receive differential gene analysis data, you will have the columns below. Briefly, the most important columns are:

• AVG_Signal: The background-corrected, normalized average signal of the feature.
• NARRAYS: The number of arrays for the group of samples (control or treated).
• ARRAY_STDEV: The standard deviation of the average signal across the arrays in that group.
• Detection Pval: The p-value of the detection of that probe. The target mRNA is considered detected if the p-value < 0.05.
• DiffScore: The significance of the difference of that probe between groups expressed as a function of p-value. Diffscore = -10*log10 p-value. So for p=0.05 the Diffscore is 13. For p = 0.01 the Diffscore is 20. For p - 0.001 the Diffscore is 30.