Introduction to Microarray analysis
From Organic Design wiki
Overview of experimental process
- Competitive hybridization to spotted oligo/cDNA transcripts
- Interested in genes that change between treatments
- → differential expression versus equivalent expression
Statistical analysis process
- Raw data (GPR file format)
- Each GPR intensity file is typically >8 megabytes
- Each TIFF image file is typically >30 megabytes
- A microarray experiment consists of several → many slides
Statistical issues
- In the past statistics was developed for n >>p
- n observations, p variables
- Gene expression data n<<p
- Thousands of measured genes (p)
- Small number of biological replicate slides (n)
- Gene expression data can be highly correlated
- groups of genes are regulated in the same way
- Data not normally distributed
- log transform highly skewed intensity data
Wish list
- Ideally would like unambiguous interpretation of results
- Large amounts of data to analyse can be overwhelming and make interpretation subjective
- Independent reproducibility of results by another collegue
- Keep a record (log) of what was done
Scratch pad
A flow diagram for analysisRecap of cDNA microarrays (slide 3)Microarray data issues (slide 4)- Microarray data issues (continued)
Large amount of data (GPR/JPEG file size)SubjectiveNeed a log of what was done so someone else can quickly reroduce the results- → Reproducible research (someone else can understand/reproduce the results) (McGintys talk)
- Analysis process
- R resources/contributed guides (including downloading)
- R tutorial of basics (objects/indexing/functions)
http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#gpr
