Difference between revisions of "Feb 9"
(Created page with "Clustering: Grouping in a particular way based on some sort of algorithm with given parameters Why cluster? Exploration of huge data, extract patterns and make predictions on...") |
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Why cluster? Exploration of huge data, extract patterns and make predictions on these patterns (hypothesis generation and testing) | Why cluster? Exploration of huge data, extract patterns and make predictions on these patterns (hypothesis generation and testing) | ||
| − | Gene expression data: | + | '''Gene expression data:''' |
Induction looks much more dramatic than the repression (be sure and remember this), equivalent on the fold change, but look very dissimilar | Induction looks much more dramatic than the repression (be sure and remember this), equivalent on the fold change, but look very dissimilar | ||
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Scatter/line plots are a different way to represent a heat map | Scatter/line plots are a different way to represent a heat map | ||
| − | Comparing Gene Expression Profiles or Guilt by expression: | + | '''Comparing Gene Expression Profiles or Guilt by expression:''' |
Co-regulation or directly regulating each other | Co-regulation or directly regulating each other | ||
| − | Proximity Measures: | + | ''Proximity Measures:'' |
Want to understand relationships genes and expression level over time or samples | Want to understand relationships genes and expression level over time or samples | ||
Correlation, Euclidean distance (distance formula), Inner product x y, Hamming distance, L1 distance, Dissimilarities may or may not be metrics | Correlation, Euclidean distance (distance formula), Inner product x y, Hamming distance, L1 distance, Dissimilarities may or may not be metrics | ||
Revision as of 19:11, 9 February 2016
Clustering: Grouping in a particular way based on some sort of algorithm with given parameters
Why cluster? Exploration of huge data, extract patterns and make predictions on these patterns (hypothesis generation and testing)
Gene expression data:
Induction looks much more dramatic than the repression (be sure and remember this), equivalent on the fold change, but look very dissimilar
A log transformation "normalizing" the way this data looks for fold changes
Negative correlations are as informative as the positive correlations
Scatter/line plots are a different way to represent a heat map
Comparing Gene Expression Profiles or Guilt by expression:
Co-regulation or directly regulating each other
Proximity Measures:
Want to understand relationships genes and expression level over time or samples
Correlation, Euclidean distance (distance formula), Inner product x y, Hamming distance, L1 distance, Dissimilarities may or may not be metrics
