qbase+ in action

Quality control

Quality control is an important feature in qbase+ and the program contains several types of quality control.

In this screenshot you see

  • quality control on technical replicates (left - top)
  • quality control on the stability of reference targets (left - middle)
  • quality control on positive and negative controls (left - bottom)
  • quality control settings window where you can define thresholds (right - top)
  • results in target bar chart for Palm target (right bottom)

qbase+ quality control screenshot

geNorm analysis

geNorm analysis enables the selection of the optimal set of reference genes from a series of tested candidate reference genes [Vandesompele et al., Genome Biology, 2002]. The qbase+ implementation of geNorm provides great benefits.

In this screenshot you see

  • geNorm M shows a ranking of candidate genes according to their stability (left - top)
  • geNorm V shows a bar chart that helps determining the optimal number of reference genes to be used (bottom)
  • Interpretation report contains a summary and interpretation of the geNorm results (right - top)

qbase+ geNorm analysis screenshot

Standard curves

The gold standard method for PCR efficiency estimation is a serial dilution of nucleic acid template.

In this screenshot you see

  • the Amplification efficiency window. qbase+ calculates the E value  from the slope of a serial dilution as follows: E = 10(-1/slope) (with an E of 2 being perfect, indicating 100% efficiency).

qbase+ standard curves screenshot

Multi-target bar chart

The Multi-target bar chart window supports the visualization of the relative expression levels between samples for multiple targets. It can be used to compare expression profiles between targets, but is explicitly not designed to compare expression levels between targets. Because of the way relative quantities are being calculated, all relationships between targets are lost. 

qbase +multi-target bar chart screenshot

Statistics

An integrated statistical analysis wizard eliminates the need for in-depth knowledge about bio-statistics.

In this screenshot you see:

  • the statistical wizard  with the first out of four easy steps that guide the user towards sound bio-statistical analysis (left - top)
  • the results in a bar chart; mean and confidence interval in the mean (right - top) 
  • the results table with p-values

qbase+ statistics screenshot

Correlation plot

qbase+ correlation plot screenshot

Copy number analysis

Quality control, normalization, copy number calling, and visualization in a single program.

In this screenshot you see

  • copy numbers visualized on a per sample basis; on top sample N1 and at bottom sample S3
  • conditional bar coloring allows for easy detection of gene copy number alterations

qbase+ CNV analysis screenshot

 

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