Correlation analysis multiomics

Is there a Galaxy tool available that allows for correlation analysis between matrices from both microbiome and gene expression data?

Welcome, @bethp

We have tutorials here to get your started.

If you would clarify the data you have now, and your research question, maybe with a publication link that describes what you would like to do? – those would all help us to point you to the right resources.

I’m going to cross-post your question over to the Micro-Galaxy chat room to bring in the scientists that work in this domain. Feel free to join the chat, too! You can use the link at the top of the tutorials or this one. → You're invited to talk on Matrix

We do have tools for correlation analysis. Such as:

and

I think you should be able to supply both matrices to: Galaxy
And get a correlation matrix between the two modality as output.

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Thanks! I am getting an error saying that my tables are not matching in sample identifiers - am I formatting my tables incorrectly? I have the sample numbers in the first row in both tables.

bact

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Thanks - I’d like to do something similar to this: Immune Gene Expression Covaries with Gut Microbiome Composition in Stickleback | mBio

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Hi @bethp

Jumping in for this technical part: your tables looks fine to me from the part that is posted. You could double check the remainder of the tables for extra spaces or columns.

A tool like this will “clean up” the whitespace in a tabular file – but this will have a problem with the internal whitespaces, so not yet.

Instead, you could try one of the Replace or Cut tools. Or, cut out the sample names and compare them with a Unique or Join tool.

I’m not sure how this tool handles whitespace in data values – the sample names will need to be oneWord1 but maybe not other labels. You could test this by replacing any internal spaces or special characters with an underscore.

As a sort of sanity check, I ran a very small test here.

You are welcome to post back your error and we can try to help more. :hammer_and_wrench:

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Thank you @jennaj ! I was able to get it to work. I had some additional samples in one table, so when I removed those and had only the samples that were shared between both datasets, it worked.

I also wanted to get the FDR p values for the correlations, and i selected this option but I am not seeing them. Was there supposed to be an additional output besides the correlation matrix and plot with the p-values? Thanks!

Hi @bethp I’m not sure and I wasn’t able to find the development repository for this tool to dig into the usage more.

Hi @paulzierep – would you be able to help? The ToolShed link to the dev repository seems too high level, my search didn’t find it (I did something wrong here probably!), and the tool xml in the ToolShed was truncated due to length… so I was mostly guessing for how to run tool tests and how use all the options.

Thanks! :slight_smile: