Affymetrix arrays

The data obtained has been derived from different experimental designs (namely, the number of collected fractions and the hybridization scheme), different microarray platforms (spotted versus Affymetrix arrays), and different data analysis schemes. In this chapter, we discuss various experimental designs for microarray analyses, provide detailed protocols for various experimental steps when using the spotted microarray platform, and discuss aspects of data analysis. 

The actual protocol for running Affymetrix arrays is very standardised - as recommended by the manufacturer. However, it is clear that this method is only... 

Affymetrix arrays are one of the most widely used platforms for transcriptional profiling. The probes are designed in silica and are synthesized directly on the array using photolithography (33, 34). Each gene (transcript) is interrogated by a probe set, which constitutes 11-20 different 25-mer perfect match (PM) probes and their corresponding mismatch (MM) probes. The MM probes differ from their PM probes by one mismatched... 

NimbleGen arrays (NimbleGen Systems, Inc., Madison, WI) are similar to the Affymetrix arrays in that they have been produced using a light-directed probe synthesis approach, but they use computer-controlled micromirrors instead of masks to... 

Affymetrix array (multiple short oligonucleotides per gene)... 

The specific way that SNPs can be identified varies between different brands. The most common ones are allele discrimination by hybridization in Affymetrix arrays (56) and allele-specific extension and ligation to a bar-code oligonucleotide hybridized to a universal array, as is done by the Illumina GoldenGate BeadArray Assay (57). 

Oudes AJ, Roach JC, Walashek LS, Eichner LJ, True LD, Vessella RL, Liu AY (2005) Application of Affymetrix array and Massively Parallel Signature Sequencing for identification of genes involved in prostate cancer progression. BMC Cancer 5 86... 

Carret, C. K., Horrocks, P., Konfortov, B., Winzeler, E., Qureshi, M., Newbold, C., and Ivens, A. (2005). Microarray-based comparative genomic analyses of the human malaria parasite Plasmodium falciparum using Affymetrix arrays. Mol. Biochem. Parasitol. 144, 177-186. 

In terms of normalization, there are many options for investigators. For Affymetrix arrays, the quantile normalization method is believed to work better on Affymetrix data at the probe cell level [23]. This method makes the assumption that the samples hybridized to the different assays have roughly the same distribution of RNA abundance over the transcripts represented on the array. This algorithm transforms the intensities so that the bulk of the intensity distribution is the same for all assays in an experiment, typically with some differences in the distribution tails (which might reflect actual biological differences). But for non-Affymetrix arrays, it is unclear which normalization method produce better results [13]. 

Genevestigator Digital Northern tools with summaries of expression in organ and tissues, during development, in response to stimuli, and in mutants based on Affymetrix arrays for Arabidopsis thaliana (>3,000 arrays) and Hordeum vulgare (>700 arrays) additional tools with subscription www.genevestigator. ethz.ch... 

NASC Array Data repository for Arabidopsis Affymetrix arrays digital Northern, other array data-mining tools affymetrix.arabidop- sis.info/narrays/ experiment- browse.pl... 

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