Summary Report
The Targeted RNA app provides an overview for all samples and groups on the Summary page. The metrics displayed in the Alignment Summary and Comparison of individual samples sections differ if viewed by individual sample or by sample group. The metrics in the Cluster Heat Map are the same for both views.
Note
To toggle these views, click the View As.. button.
Cluster Heat Map
Click and drag on gene or samples names to change the displayed region of the heat map. When the cursor is over a gene or sample name, the mouse wheel can be used to zoom in and out. Clicking a specific gene name displays additional information for that amplicon.
All samples and amplicons are jointly clustered to produce a single clustering result. Before clustering, the following normalizations are performed:
| • | Application of a minimum count threshold of 1 |
| • | Log transformation of counts |
| • | Median normalization of counts across samples |
Agglomerative hierarchical clustering is then performed on the normalized values using correlation as the distance measure along with average linkage. Following clustering, the data are MAD-normalized within each amplicon for display.
Alignment Summary, Sample Group View
The Alignment Summary provides a table with metrics and a graph of aligned reads per group. The metrics displayed in Group View are described in the following table:
| Statistic | Definition |
|---|---|
| Group Index | Group number |
| Sample Group | Sample group as specified in input form |
| # Replicates | Number of samples assigned to this sample group |
| Total Aligned Reads (R1/R2) | The total count of PF reads aligning for the group (Read 1/Read 2) |
| Percent Aligned Reads (R1/R2) | Percentage of PF reads aligning for the group (Read 1/Read 2) |
| Overall Percent Aligned Reads | Percentage of PF reads aligning for the group across both reads 1 and 2 |
Alignment Summary, Individual Sample View
The Alignment Summary provides a table with metrics and a graph of aligned reads per sample. The metrics displayed in Sample View are described in the following table:
| Statistic | Definition |
|---|---|
| Sample Index | Sample number |
| Sample Id | Sample identifier |
| Sample Group | Sample group as specified in input form |
| Total Aligned Reads (R1/R2) | The total count of PF reads aligning for the group (Read 1/Read 2) |
| Percent Aligned Reads (R1/R2) | Percentage of PF reads aligning for the group (Read 1/Read 2) |
| Overall Percent Aligned Reads | Percentage of PF reads aligning for the group across both reads 1 and 2 |
Comparison of individual samples, Sample Group View
Under Comparison of individual samples, you can view pairwise differential expression between all pairs of sample groups. Select the comparison for display in the drop-down box. You can view the following metrics:
| • | The Normalized read count comparison is a scatter plot comparison of the normalized read counts between the two sample groups. |
| • | The Differential expression results table provides a comparison between the two sample groups per gene or transcript. The table displays the following metrics: |
| Statistic | Definition |
|---|---|
| Assay ID | Unique ID for each amplicon |
| Gene | Gene targeted by assay |
| Transcript | Transcript targeted by assay |
| Left Exon | Left exon of targeted region |
| Right Exon | Right exon of targeted region |
| Normalized Count 1, 2 | Averaged and normalized count across samples in group 1 and 2, respectively |
| Fold Change | Fold change of normalized read counts between groups 1 and 2 |
| p-val | P-value of differential expression between groups 1 and 2 |
| q-val | Q-value of differential expression between groups 1 and 2 |
Comparison of individual samples, Individual Sample View
Under Differential expression between sample groups, you can view pairwise differential expression between all pairs of sample groups. Select the comparison for display in the drop-down box. You can view the following metrics:
| • | The Normalized read count comparison is a scatter plot comparison of the normalized read counts between the two samples. |
| • | The Differential expression results table provides a comparison between the two sample groups per gene or transcript. The table displays the following metrics: |
| Statistic | Definition |
|---|---|
| Assay ID | Unique ID for each amplicon |
| Gene | Gene targeted by assay |
| Transcript | Transcript targeted by assay |
| Left Exon | Left exon of targeted region |
| Right Exon | Right exon of targeted region |
| Sample 1, 2 Normalized Count | Normalized counts for sample 1 and 2, respectively |
| Log Ratio | Ln (Sample 1 Normalized Count/Sample 2 Normalized Count) |