HLab:Rscripts

Miscellaneous R Scripts

Quantile normalization

• This can be used directly or as an example. It takes an input and output file names (tab-delimited files with header and row names). It is set up for RNA and adds 1.1 to the expression levels to avoid zeros before taking the log2(normalized expr). Media:normalize.r.txt

Scatter plots for replicates

• This is an example. File names and number of columns are hard coded and will need changed to match your usage. The first one plots the points all the same color. For graphs that are very dense the second one changes the colors depending on the number of bins in the vicinity of the one being plotted (red is dense).
  • plotPairs.r
  • plotPairsDensity.r

PCA

GEDI

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