Any strategies to compare gene and protein expression dataset and perform differential expression

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2.8 years ago

vin23 ▴ 10

Hello all, I am new to R programming and I would like your help in suggesting a strategy to solve the following question.

I have gene expression data and protein expression data which has the same samples. I want to identify differentially expressed genes by comparing both datasets. So for this I have tried first merging both the datasets and performing differential expression using limma, then I have also tried taking ratio or gene: protein and performing a differential expression using limma. All these strategies were not successful as I got a weird volcano plot as I have attached below. I would be very grateful if someone suggest me a strategy or a method by which I can perform this analysis.

volcano plot of the ratio of gene: protein analysis

gene-expression R protein-expression Differential-gene-expression Volcano-plot • 1.0k views

ADD COMMENT • link updated 7 months ago by Ram 44k • written 2.8 years ago by vin23 ▴ 10

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You cannot merge these datasets, it's completely different technologies with different characteristics and types of measurements. You can analyse them separately and then see how the DEGs from the transcriptome experiment behave in the proteome and vice versa.

ADD REPLY • link 2.8 years ago by ATpoint 85k

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