How to extract the voom normalized value for each observation?

Question

[harelarik]

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.

Answer 1

[harelarik]

See answers in: https://support.bioconductor.org/p/103747/#103769