This tool evaluates the difference in expression level of genes for two experimental conditions and highlights those for which this difference is statistically significant. Results can be obtained by following 6 steps, described below:
- 1. Choose an oraganism and one or several reference sequences.
- 2. If several choices are available, you can choose the mapping strategy.
- 3. If several choices are available, you can choose the experimental protocol.
- 4. The p-value adjusted (padj) column contains the p-values, adjusted for multiple testing with the Benjamini-Hochberg procedure (see the standard R function p.adjust), which controls false discovery rate (FDR) . It’s possible to restrict the result for the ones which are under a fixed FDR cut-off. Example : A FDR adjusted p-value (or q-value) of 0.05 implies that 5% of significant tests will result in false positives.
- 5. Select at least one B condition to compare to A condition (which will be used as reference).
6. Graphical Option :
- Choose to have all the fields of the result table or a light version. The fields will be fully described in the next section.
- If several B conditions are chosen, the fixed FDR cut-off can be fixed in all comparisons or in at least one comparisons for each gene.
Case 1 : One B condition selected.
1. Export functions. This section allows users to make all genes (or subsets of genes) available for other analysis tools. 3 main operations are possible here:
- Select subsets of genes (by selecting checkboxes on the first column) and export them into a
Gene Cart <genecarts>
by using the “Export To Gene Cart” button. - See one selected gene into the
MaGe Genome Browser <viewer>
by clicking on the magnifying glass. - Direct link to the selected gene in Integrative Genome Viewer.
- Direct link to MeV.
- Direct link to MicroCyC.
- Select subsets of genes (by selecting checkboxes on the first column) and export them into a
- 2. The second part reports the main genomic object features : Label (Link to more Genomic Object information), Type, Name, Product, Begin, End, Length, Frame.
3.
- Light Result part: Normalized average read count, log2foldchange, adjusted p-value, FDR (all the result are under the chosen value)
- DESeq Module Result part:
- baseMean = normalized average read count.
- baseMeanA = normalized average read count for condition A.
- baseMeanB = normalized average read count for condition B.
- foldChange .
- log2foldchange.
- p-value = non adjusted pvalue.
- padj = adjusted p-value, FDR (all the result are under the chosen value)
- resVarA et resVarB = These columns contain the ratio of the variance as estimated from the counts for just this gene over the -* variance as predicted from the mean.
All these results are fully described in : http://bioconductor.org/packages/2.6/bioc/vignettes/DESeq/inst/doc/DESeq.pdf
Case 2 : Two B conditions or more selected.
Users can choose to see the union or intersection result.