Other parameters

The sortBy argument specifies the criterion used to select the top genes. The choices are: ``M'' to sort by the (absolute) coefficient representing the log-fold-change; ``A'' to sort by average expression level (over all arrays) in descending order; ``T'' for absolute $ t$-statistic; ``P'' for p-values; or ``B'' for the ``lods'' or $ B$-statistic.

Normally the genes appear in order of selection in the output table. If one wants the table to be in a different order, the 'resort.by' argument may be used. For example, sortBy=``B'', resortBy=``M'', selects the top genes according to log-odds of differential expression and then orders the resulting genes by log-ratio in decreasing order. Or sortBy=``M'', resortBy=``M'' would select the genes by absolute log-ratio and then sort then by signed log-ratio from must positive to most negative.



Bjørn Kåre Alsberg 2006-04-06