Hello everyone, I have been asked to summarise information from my count matrix - obtained from 4 replicates - in just two columns (one column per group). What's the best approach to do this? I usually use the following steps to get a classical heatmap containing as many tiles as per replicate
top <- head(order(-rowVars(assay(rld))),100)
and then I take out the row mean
mat <- assay(rld)[ top, ] mat <- mat - rowMeans(mat)
Once I got what I want I use heatmap.2 to plot my results.
Since I have already applied the mean centring here, if I wanted to present my data as just two separate columns (thus merging values from each replicate in just one tile/condition), I should take the average from each group (i.e. condition 1 and condition 2); in this way I always get almost 'specular' results and I don't think it is correct to do this way. Any ideas?