1. Vicky Fan, Bioinformatics Institute

2.  Solid surface which the sequences from thousands of different genes (or proteins) are attached at fixed locations  DNA, cDNA, or oligonucleotides  2-colour and single colour arrays

3.  something: ◦ Something else  Something ◦ Something else ◦ Something something else  Stuff ◦ More stuff

5.  Check the microarrays look OK

6. Culprit to be identified ?

7.  Check the microarrays look OK

8.  Normalise and summarise the data  Check that the normalised data looks OK

9.  Differential expression analysis  Correct for multiple testing Treatment ATreatment B A1B1 A2B2 A3B3 A4B4 A5B5 A6B6 A7B7 A8B8 A9B9 A10B10

10. Model parameters Hypothesis strength data Transcript information

12. MicroarraysNext Generation Sequencing Established technologyNew technology Can only detect transcripts with probes present on array – usually mRNA, miRNA Measures all assembled transcripts – mRNA, ncRNA, etc Species specific – need to be made for a specific species/condition Can sequence any species Does not generally detect alternative splicing Can detect alternative splicing CheapExpensive (getting cheaper) Lots of existing results for comparison Mature technology: well established methods of analysis New technology: no one is really sure how to analyse the data.

13. Thank you! Vicky Fan, Bioinformatics Institute v.fan@auckland.ac.nz