It depends on which method produced them. By Cell scores each gene set in each cell. iSCanGuide z-scores every gene within the cell, then compares the genes in your selected set against the genes in all the other sets you [...]
Most analyses in iPathwayGuide complete within 15 minutes, depending on dataset size. If yours has been running noticeably longer, check that you don't have the same report open in more than one browser tab, as that's a known way to [...]
Exported figures are generated at publication-ready resolution, which can look different in size or layout from the on-screen preview. If your download is unexpectedly large, has extra white space, or is missing something visible on screen, that's a known issue [...]
log2(Fold Change) is the standard input, so the Fold Change column should be log2-transformed. iPG can take in raw p-values, and adjusted (multiple-test corrected) p-values, we recommend using adjusted p-values.
Different views in your report can apply different thresholds, gene subsets, or statistical layers, so the same gene or pathway can show slightly different values depending on which chart or tab you're viewing. If numbers disagree in a way that [...]
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