Integrate transcriptomic data and proteomics data.

Question

[이민경[학생](대학원 융합의과학과)]

Hello, I'm a student new to bioinformatics. First, we have transcriptomics data with three replicates and proteomics data with two replicates. I would like to combine these two types of data to create omics data. Since there are three types of transcriptomics and two types of proteomics, I'm wondering what method can be used to integrate these datasets. Second, the transcriptomics data has over 20,000 gene information, and the proteomics has about 1,000 gene information. I'm curious about the potential issues that might arise during the integration process and how to correct them. I mainly use R programming and would like to know how to address these issues using R.

[Lluís R.]

You don't need to subset for common features, there are tools that work for that like RGCCA, mixOmics. See for instance a classification here, and a list of tools here, some tools use network approaches if the variables are the same.

[Ram]

Please define "combine" and "integrate" as best as you can. How do you picture the final product of this task?

Answer 1

[KABILAN]

You can use R package named 'mixOmics' to integrate the datasets. Kindly go through the manual of this package.