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 microarray 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 microarray 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-types (A and B) profiled by ImmGen microarray. Drag and drop the cell-types to each Group (A or B), click "Submit" and wait a few seconds.
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). To interpret the mean_A and mean-B expression values, recall that in ImmGen microarray data values of 120 or greater mean true expression, while values of 32 or below are almost certainly background (and those in between are uncertain). 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). To interpret the mean_A and mean-B expression values, recall that in ImmGen microarray data values of 120 or greater mean true expression, while values of 32 or below are almost certainly background (and those in between are uncertain). 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.
Datasets:
