Difference between revisions of "Introduction to Microarray analysis"
From Organic Design wiki
m |
(→Scratch pad: items done) |
||
| Line 26: | Line 26: | ||
====Scratch pad==== | ====Scratch pad==== | ||
| − | * A flow diagram for analysis | + | * <s>A flow diagram for analysis</s> |
| − | * Recap of cDNA microarrays (slide 3) | + | * <s>Recap of cDNA microarrays (slide 3)</s> |
| − | *Microarray data issues (slide 4) | + | *<s>Microarray data issues (slide 4)</s> |
*Microarray data issues (continued) | *Microarray data issues (continued) | ||
**Large amount of data (GPR/JPEG file size) | **Large amount of data (GPR/JPEG file size) | ||
Revision as of 02:09, 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 analysisRecap 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)
