Testing for specific genes of whole RNA Sequencing

Question

[hagl]

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.

Answer 1

[ATpoint]

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.