Difference between revisions of "Introduction to Microarray analysis"
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[[Image:expt2.tiff|thumb|500px|''Courtesy Mik Black'']] | [[Image:expt2.tiff|thumb|500px|''Courtesy Mik Black'']] | ||
*Competitive hybridization to spotted oligo/cDNA transcripts | *Competitive hybridization to spotted oligo/cDNA transcripts | ||
| − | *Interested in genes that change between | + | *Interested in genes that change between treatment conditions |
:<font color="blue">→ ''differential expression versus equivalent expression''</font> | :<font color="blue">→ ''differential expression versus equivalent expression''</font> | ||
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====Statistical analysis process==== | ====Statistical analysis process==== | ||
[[Image:overview2.tiff|thumb|500px|''Analysis workflow from scanner to results'']] | [[Image:overview2.tiff|thumb|500px|''Analysis workflow from scanner to results'']] | ||
Revision as of 21:22, 14 March 2006
Overview of experimental process
- Competitive hybridization to spotted oligo/cDNA transcripts
- Interested in genes that change between treatment conditions
- → 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
Analysis aim
- Easier to rank genes in order of evidence of differential expression than it is to select a specific cutoff
- If we do select a cutoff, False Discovery Rate (FDR) cutoff is usually used
- FDR threhold is the expected proportion of genes in a list that are likely to be incorrect
TODO: Picie of a gene list
