Unfiltered DE results
i
Your genes will be ranked to perform Gene Set Enrichment Analysis.
Different ranking methods will give different gene sets enrichment scores.
Different ranking methods will give different gene sets enrichment scores.
Rank by
i
This is a BH (Benjamini & Hochberg) FDR (false discovery rate) adjusted p-value for gene sets enrichment scores. It differs from adjusted p-values of the gene expression results above.
Any gene sets with adjusted p-values above a chosen FDR threshold will be omitted from the enrichement results.
Any gene sets with adjusted p-values above a chosen FDR threshold will be omitted from the enrichement results.
P adjusted
≤
database
PCA plot of VST transformed data
Shows clusters of samples based on their similarity. PC1 representing the most variation in the data. PC2 representing the second most variation in the data.
Dispersion estimates plot
As the read count gets higher usually there is less variation, so we can see a decreasing slope.
Sparsity plot
Shows the concentration of counts in a single sample over the sum of counts per gene.
Filters
DE results filters
i This section is designed for flexible filtering of the DE results table.
i
????
pvalue
<
+NA
i
BH adjusted p-value.
padj
<
+NA
i
log2FC is the effect size estimate. It tells us how much the gene’s expression seems to have changed.
This value is reported on a logarithmic scale to base 2: e.g., for a particular gene, a log2 fold change of −1 for condition treated vs untreated means that the treatment induces a change in observed expression level of 2^−1 = 0.5 compared to the untreated condition.
This value is reported on a logarithmic scale to base 2: e.g., for a particular gene, a log2 fold change of −1 for condition treated vs untreated means that the treatment induces a change in observed expression level of 2^−1 = 0.5 compared to the untreated condition.
+NA
i
????
lfcSE
>
+NA
i
Mean of normalized counts of all samples.
baseMean
>
+NA
i
????
+NA
i
Average expression across all samples.
AveExpr
>
+NA
i
????
+NA
i
????
+NA
Select gene sets to filter by:
Filtered DE results
This table contains filtered DE results.
xlsx
i
Your genes will be ranked to perform Gene Set Enrichment Analysis.
Different ranking methods will give different gene sets enrichment scores.
Different ranking methods will give different gene sets enrichment scores.
Rank by
i
This is a BH (Benjamini & Hochberg) FDR (false discovery rate) adjusted p-value for gene sets enrichment scores. It differs from adjusted p-values of the gene expression results above.
Any gene sets with adjusted p-values above a chosen FDR threshold will be omitted from the enrichement results.
Any gene sets with adjusted p-values above a chosen FDR threshold will be omitted from the enrichement results.
P adjusted
≤
database
Pathway enrichment table
Select pathway of your interest in order to see more details
xlsx