Difference between revisions of "Introduction to Microarray analysis"
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====Overview of experimental process==== | ====Overview of experimental process==== | ||
| − | [[Image:expt2.tiff|thumb|400px|'' | + | [[Image:expt2.tiff|thumb|400px|''Courtesy Mik Black'']] |
*Competitive hybridization to spotted oligo/cDNA transcripts | *Competitive hybridization to spotted oligo/cDNA transcripts | ||
*Interested in genes that change between treatments | *Interested in genes that change between treatments | ||
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====Statistical analysis process==== | ====Statistical analysis process==== | ||
| − | [[Image:overview2.tiff|thumb|400px|Analysis workflow from scanner to results]] | + | [[Image:overview2.tiff|thumb|400px|''Analysis workflow from scanner to results'']] |
---- | ---- | ||
====Data issues==== | ====Data issues==== | ||
*In the past statistics was developed for n >>p | *In the past statistics was developed for n >>p | ||
| − | :<font color=" | + | :<font color="blue">n observations, p variables</font> |
*Gene expression data n<<p | *Gene expression data n<<p | ||
| − | + | :<font color="blue">Thousands of measured genes (p)</font> | |
| − | + | :<font color="blue">Small number of biological replicate slides (n)</font> | |
*Gene expression data can be highly correlated | *Gene expression data can be highly correlated | ||
| − | + | :<font color="blue">groups of genes are regulated in the same way</font> | |
*Data not normally distributed | *Data not normally distributed | ||
| − | + | :<font color="blue">log transform highly skewed intensity data</font> | |
| − | [[Image:Graph channels.tiff|thumb|200px|Density plots from a 16-bit scanner]] | + | [[Image:Graph channels.tiff|thumb|200px|''Density plots from a 16-bit scanner'']] |
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Revision as of 02:08, 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
Data 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
Scratch pad
- A flow diagram for analysis
- Recap of cDNA microarrays (slide 3)
- Microarray data issues (slide 4)
- Microarray data issues (continued)
- Large amount of data (GPR/JPEG file size)
- Subjective
- Need 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)
