View significant condition list

While getOutputForPCNOutliers() lists interesting extreme points and can show interesting patterns along the rows of a dataset, getOutputForSigGroups() displays the conditions in the extreme gene data-driven ordering, specifically ordered by mean(high) - mean(low). Conditions are

Unfortunately the yeast cell cycling dataset only has one covariate, time (the "time points" column labeling), so it is not really a good example of this feature.

pcaginzu.getOutputForSigGroups(1, ['time points'])

PC-1 10-outlier Up/Flat/Down Columns times
up 7 h
up 8 h
up 6 h
up 15 h
up 16 h
up 14 h
up 5 h
flat 13 h
flat 4 h
flat 0 h
down 9 h
down 12 h
down 10 h
down 11 h
down 3 h
down 1 h
down 2 h

If one looks carefully one can start to see hints of the cell cycle that was captured by this output. It is most instructive to look at the top and bottom of the list where the differences are greatest. At the top, at 6,7,8 hours we observe the strongest high over low differences. At the other end of the condition list, at a completely different phase of the cell cycle, hours 1,2,3 show strongest low over high (or "down") conditions. This is also evident in the corresponding trajectory plots:


Joe Roden 2005-12-13