Difference between revisions of "Introduction to Microarray analysis"
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| − | ====Overview of process==== | + | ====Overview of experimental process==== |
[[Image:expt2.tiff|500px]] | [[Image:expt2.tiff|500px]] | ||
*competitive hybridization to spotted oligo/cDNA transcripts | *competitive hybridization to spotted oligo/cDNA transcripts | ||
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:→ ''differential expression versus equivalent expression'' | :→ ''differential expression versus equivalent expression'' | ||
---- | ---- | ||
| + | ====Statistical analysis process==== | ||
[[Image:overview2.tiff|thumb|Analysis workflow from scanner to results]] | [[Image:overview2.tiff|thumb|Analysis workflow from scanner to results]] | ||
| + | ---- | ||
| + | ====Data issues==== | ||
| + | *In the past statistics was developed for n >>p | ||
| + | :<font color=blue">n observations, p variables</blue> | ||
| + | |||
| + | *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==== | ====Scratch pad==== | ||
* A flow diagram for analysis | * A flow diagram for analysis | ||
Revision as of 01:53, 14 March 2006
Contents
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</blue>
- 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)
