The Signal Searching Criteria dialog opens after you click the Choose Signal Criteria button during Advanced Filtering. This dialog allows you to set confidence levels based on a variety of variables.
•Make selections from the three menus: Signal Set, Signal Type and Scale.
If you used DESeq2 normalization and are filtering based on Expression Level/Signal or Signal Sample Group, the Signal Set menu offers a subset of the following DESeq2 statistics:
o rlog reads
o adjusted P value
o base mean
o lfc SE
o raw P value
o Wald stat
o log2 fold change
Note: Fold change values obtained through Advanced Filtering will vary from the log2 values in the Isoform or Gene tables. Fold change calculation in the Advanced Filtering dialog uses a simple arithmetical formula based on the read counts and uses a linear scale. By comparison, DESeq2-generated statistics, including the log2 fold change, are based on a probabilistic model that uses the raw read counts as input, but then runs complex statistics to yield a collection of metrics.
•To the right of Signal, choose a mathematical symbol and type in the desired signal threshold.
Click OK to save your changes and return to the Advanced Filtering dialog. Choose Cancel to leave the dialog without saving your changes.