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*weight of each observation? (just multiplication?)? How should I combine the sample weight?