Difference between revisions of "Introduction to Microarray analysis"
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Revision as of 03:21, 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 http://www.moleculardevices.com/pages/software/gn_gpr_format_history.html)
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)
http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#gpr
