Comparison between multiple populations
This analysis returns the genes that are differentially expressed between groups of populations (A and B).
The simple logic of pairwise comparisons do not apply here, and there are several stringency settings to compare the two groups: should the selected genes be expressed in all of the A populations ("Always") or only in some ("Sometimes"); should they be completely absent from the B group ("Never") or is some expression acceptable ("Sometimes"). Expression is defined relative to an adjustable threshold: for ImmGen data, 120 (default threshold) is a conservative threshold for true expression (0.95 probability that a gene is expressed), 32 a conservative threshold for non-expression (0.95 probability that a gene is at background level). The FoldChange metric to be calculated can be chosen as: ratio of means, ratio of maxs, or minA/maxB (most stringent, gives the smallest differential)
No statistical values are returned in this case, because the computation does not use population replicates and because it would not make sense to compute a t.test or an FDR on differently sized groups of mixed populations.
The simple logic of pairwise comparisons do not apply here, and there are several stringency settings to compare the two groups: should the selected genes be expressed in all of the A populations ("Always") or only in some ("Sometimes"); should they be completely absent from the B group ("Never") or is some expression acceptable ("Sometimes"). Expression is defined relative to an adjustable threshold: for ImmGen data, 120 (default threshold) is a conservative threshold for true expression (0.95 probability that a gene is expressed), 32 a conservative threshold for non-expression (0.95 probability that a gene is at background level). The FoldChange metric to be calculated can be chosen as: ratio of means, ratio of maxs, or minA/maxB (most stringent, gives the smallest differential)
No statistical values are returned in this case, because the computation does not use population replicates and because it would not make sense to compute a t.test or an FDR on differently sized groups of mixed populations.
Differential Expression Analysis
This analysis brings up the genes that are differentially expressed between two cell populations (A and B): either different cell-types, or the same cell-type in genetic or other variants.
The results returned include FoldChange (ratio of A/B expression) and common significance statistics (t.test p.value and FalseDiscoveryRate based on comparison of replicates). Select the two populations over to each "Group" by drag and drop, click "Submit" and wait 5 seconds. The result table can be ordered according to any parameter (click on the heading), and downloaded (click below). The expression profile of individual genes can be visualized by clicking a row of interest in the result table.
The results returned include FoldChange (ratio of A/B expression) and common significance statistics (t.test p.value and FalseDiscoveryRate based on comparison of replicates). Select the two populations over to each "Group" by drag and drop, click "Submit" and wait 5 seconds. The result table can be ordered according to any parameter (click on the heading), and downloaded (click below). The expression profile of individual genes can be visualized by clicking a row of interest in the result table.
