I want to normalize metabolomics 'counts' data by Variance Stabilizing Transformation. In the meantime I already did that by VST function of using DESeq package and this improve in my opinion the clustering between replicates on a PCA plot which make sense for me. However I just wonder if I need actually use some modification on the function to avoid include library size normalization and what is different regarding the old VSN function of Limma package. Maybe I should be use that instead the implemented VST on DESeq? I mean; Is DESEq using a wrapper of VSN Limma for permom the VST or doing something else to normalize by library size? Any comment regarding my approach will be appreciated guys,
Question: Is right normalize metabolomics "counts" by Variance Stabilized Transformation using VST DESeq2 package function?
22 months ago by
panconchoclo • 10
panconchoclo • 10 wrote:
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