Difference between revisions of "Introduction to Microarray analysis"
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[[Image:Graph channels.tiff|right|thumb|250px|''Density plots from a 16-bit scanner'']] | [[Image:Graph channels.tiff|right|thumb|250px|''Density plots from a 16-bit scanner'']] | ||
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* Ideally would like unambiguous interpretation of results | * Ideally would like unambiguous interpretation of results | ||
* Large amounts of data to analyse can be overwhelming and make interpretation subjective | * Large amounts of data to analyse can be overwhelming and make interpretation subjective | ||
Revision as of 04:02, 14 March 2006
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
Analysis 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
