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Component
DuplicateQualityEstimates microarray chip quality by printing expression distributions for duplicate probes. The assumption is that duplicate probes should have similar expression values and high variance indicates quality problems.
The report contains a table for each column in 'expr' that shows distribution parameters for some of the most frequent duplicate probes. Also, there is a spatial plot for each column that contains z-values for all duplicate probes. Z-values are derived with the formula Z = (X-median) / SD, where X is the raw value of the spot in question and median and SD are distribution parameters for the probe class. The figure shows the z-value range from -2 (green) to 2 (red).
| Version | 1.0 |
|---|---|
| Bundle | microarray |
| Categories | Quality Control |
| Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R |
| Source files | component.xml DuplicateQuality.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| expr | LogMatrix | Mandatory | Expression data. |
| geneAnnotation | AnnotationTable | Mandatory | Must contain the column named by the parameter column. Values from this column are used to detect duplicates. Also must contain the columns Row and Col. |
Outputs| Name | Type | Description |
|---|---|---|
| report | Latex | Quality report. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| column | string | "ProbeName" | Column name in geneAnnotation that is used to identify duplicate probes. All spots that have the same ID are considered duplicates. |
Test cases| Test case | Parameters▼ | IN expr |
IN geneAnnotation |
OUT report |
||
|---|---|---|---|---|---|---|
| case1 | properties | expr | geneAnnotation | report | ||
|
column=Name |
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