EdgeR in Galaxy. Adjust C-value?

Question

[ando.kelli]

Hey all,

I'm using an EdgeR suite (https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki) in Galaxy to look at differential expression of RNA-seq data.

I'm just wondering what the C-value in the 'Analyze_Differential_Expression' tool in the last step is used for? It doesn't explain it in the wiki, and I've not read anything about a C-value in the Bioconductor manual.

I have a feeling it might be something to do with the fold change cutoff for extracting data. In the github protocol the author is looking for genes that have a minimum of a 4 fold difference, and they use a C-value of 2 to extract the data.

Thanks!

Kelli

Answer 1

[Devon Ryan]

Wow, that's really poorly documented. Their made up C-value term turns out to be what everyone else in the world calls the absolute value of the log2 fold-change. So a value of 2 means >=4x difference in either direction. This is only documented here, which they couldn't have expected you to find.

[ando.kelli]

Hi Devon,

Thanks so much for getting back to me! That clears it up perfectly!

Kel