Dear community,
I want to combine proteomic and transcriptomic data for my project.
Since there are only 40 proteins measured in the assay I am wondering if I can just extract the normalized counts from my DESeq2 object and apply a Wilcox rank sum test or if it is recommended to extract LFCs and p_values/adjusted p_values after DESeq2 procedures (from negativ binomial model).
Thank you for your assessments.
1 answer
The problem with the Wilcox test is that it has lower power at low sample size. That is where the likes of DESeq2 (and other tools) come in -- borrowing information from all genes to better estimate the overall mean-variance trend. What you get from these tools is typically more reliable that simple tests such as the Wilcox unless your sample size is really large. I would (without more context given) use the output of DESeq2.
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