Paired Statistical Analysis

[edunivers]

We tried to make paired analyses using the experimental_annotation column "replicate", but this setup

condition	replicate
A	1
A	2
A	3
B	1
B	2
B	3

gives the same statistical results that setting the annotation file to:

condition	replicate
A	1
A	2
A	3
B	4
B	5
B	6

Is FragPipe-Analyst to do paired analysis? How should we encode the pairs in the annotation file?

[hsiaoyi0504]

@edunivers FragPipe-Analyst doesn't support paired analysis yet but @Hailey-Z Is that something already implemented in LFQ-analyst? Any chance we can bring that feature here?

[Hailey-Z]

Hi @edunivers, as @hsiaoyi0504 mentioned, you can do the paired analysis in LFQ-Analyst (Dev version) from our Analyst Suites landing page, which is also compatible with LFQ output from FragPipe. @hsiaoyi0504 we can also add this feature here if you are happy with that.

You can annotate the replicates as what you showed in the first table. After uploading your experimental design file, there will pop-up options for paired test analysis. In addition to that, you can also add other factor columns in your experimental design file (e.g. gender) if applicable. Please don't hesitate to reach out to me if you have any questions in your analysis (hailey.zhang1@monash.edu). Thank you.

[edunivers]

Thanks for the answer. It would be fantastic if this feature could be implemented also in the FragPipe-Analyst tool.

[hsiaoyi0504]

@Hailey-Z That's nice. Be sure to use the latest main branch. I have a major update recently on modifying how to use make_unique function.