User:Pisanu Buphamalai/Notebook/TF affininties vs nuleosome affinities/2011/09/15

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Instruction

  • The attached file described the affinity of a yeast TF called Hap1, throughout the yeast genome (column 3-5), and nucleosome binding affinity (column 6-8). The values represent maximum, average, and median of 32 base pair window. Notice that the values are not available for all the base pairs but only for every 32 base pairs.

1. The original file is large so it was split and compressed. Decompressed the files and combine them in R or notepad.

2. Find correlation of TF affinities vs nucleosome affinities, for different categories (max, avg, med). That is, correlate column 3 to 6, 4 to 7, and 5 to 8. Do they give the same/different results?

3. How many types of correlation coefficients are available (e.g. Pearson, Spearman)? Do they return similar coefficient?

4. Do the three nucleosome affinity types (column 6-8) significantly different from one another? What statistic can be used to assess?