DE analysis with multiple factors

DE analysis with multiple factors

0

Hi all,

I’m using DEP R package to perform analysis (including DE analysis) on proteins across different conditions
bioconductor.org/packages/devel/bioc/vignettes/DEP/inst/doc/DEP.html

The package uses limma for DE analysis

My experiment is structured as :

sample – disease_state( disease / healthy) – environment (env1 / env2)

I wish to perform DE analysis for

  1. env1 Vs env2 samples
  2. within diseased, env1 vs env2 samples
  3. within healthy, env1 vs env2 samples

For 1, I’m just ignoring the disease_state factor and performing differential expression analysis across conditions env1 vs env2. Is this the correct approach ?

For 2, filter out only diseased samples and then then perform differential expression analysis across conditions env1 vs env2. Is this correct ? or do all the healthy samples also need to be somehow included so as not to lose information ?

Please do share any articles which would explain the fundamentals in terms of why one of these approaches are incorrect


DE


DEP


limma

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