How to extract the voom normalized value for each observation?
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:
- The $E should actually be: logCpm+0.5 for each gene regardless of voom normalization.
That does not include the voom normalization.
- weights- are "numeric matrix of inverse variance weights" .
These are probably only the weights for each observation (observation= gene X sample).
- $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.
1 answer
See answers in: https://support.bioconductor.org/p/103747/#103769
Log in to answer this question.
More posts like this
-
Confused with EdgeR TMM normalization
written by joelking •
-
edgeR customized normalization for differential analysis
written by Wu-Sheng Zhang •
-
limma voom -- all genes after filtering are differentially expressed
written by wiscoyogi •
-
adjusting for confounding factors in Spearman correlation?
written by diogo.moraes •
-
What does one do with voom precision weights when scaling expression data
written by seankpurcell •
-
voom variance modeling: lowess curve fitting notation wrong?
written by njbernstein •
-
How to convert RNA-seq data to microarray data as if it was microarray data
written by shuyong •
-
Meta-analysis in PLINK - What to use in order to do a forest plot
written by GabrielMontenegro
-
PCA of a genotype matrix
written by oselm •
-
Weights for dependent variable using limma voom
written by lkmklsmn
