Partek Flow Documentation

Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

    1. Remove all the features that have 0 read reads in all samples.
    2. Get the upper quartile in each sample, and divide the upper quartile by the total count of the sample.
    3. Upper quartile of a sample is scaled by the geometric mean of the upper quartile across all the samples.
    4. Raw reads of a sample on a feature is divided by the scaled upper quartile of the sample.Calculate the effective library size per sample: effective library size = (upper quartile for a particular sample) / (geometric mean of upper quartiles in all the samples) * (raw library size (in millions))
    5. Get the normalized counts by dividing the raw counts per feature by the effective library size (for the respective sample)

Normalization Report

The Normalization report includes the Normalization methods used, a Feature distribution table, Box-whisker plots of the Expression signal before and after normalization, and Sample histogram charts before and after normalization. Note that all visualizations are disabled for results with more than 30 samples.

...