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I need to plot microarray time course data so that the gene expression profiles of the top 100 genes are shown on the graph, with the curves labeled with the replicate probes (information below).

I was able to draw the graph frames with the right titles and axes labels, but label on the curves did not have the right names, using the following code:

  for(j in 1:12){
  pch_value = as.character(targets$grp[6*j])
  points(c(0, 6, 24, 48, 72,80), exprs.row[(6*j-1):(6*j)],
  type='b', pch=pch_value)

Contrasts:

mc = makeContrasts("hr6-hr0","hr24-hr0","hr48-hr0","hr72-hr0","hr80-hr0","hr72-hr6", levels = X)



colnames(X) = c('hr0', 'hr24', 'hr48', 'hr6', 'hr72', 'hr80')

Replicate information:

Replicates (hr0 - 6 reps, hr 6 - 6reps, hr24-4reps, hr48-4reps,hr72-6reps, hr80-2reps) are in the following order :
hr0
hr0
hr6
hr6
hr24
hr24
hr48
hr48
hr72
hr72
hr0
hr0
hr6
hr6
hr24
hr24
hr48
hr48
hr72
hr72
hr80
hr80
hr0
hr0
hr6
hr6
hr72
hr72

I have tried maSigPro and timecourse; I was unable to set the correct contrasts using these two programs.

Help will be appreciated.

user27976
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  • The ` levelplot' function may be a better solution. http://stackoverflow.com/questions/13895480/how-to-show-matrix-values-on-levelplot – user1436187 Oct 02 '13 at 01:59
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    I tried to copy and paste your code into my own setup but the code/data are not reproducible. What is the `target` object? Please read [this post](http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) as it will show you how to create a reproducible question that will get you more and better answers. – SlowLearner Oct 02 '13 at 06:42

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