How to extract the voom normalized value for each observation?
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6.4 years ago
harelarik ▴ 90

I want to use the output values of voomWithQualityWeights as an input for further analysis (e.g., input for network).

The outputs of voomWithQualityWeights are:

  1. The $E should actually be: logCpm+0.5 for each gene regardless of voom normalization. That does not include the voom normalization.
  2. weights- are "numeric matrix of inverse variance weights" . These are probably only the weights for each observation (observation= gene X sample).
  3. $sample.weights- weight normalization per sample.

How do I extract the voom normalized value for each observation?
Is it $E of each observation multiplied by weight of each observation? (just multiplication?)? How should I combine the sample weight?

Thank you.

outputvoomwithqualityweights • 4.1k views
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