How to get log fold change for individual samples?


I’m trying to analyses RNAseq data from 8 samples (4 Control and 4 treatment) using lime/DESeq2 and the information that is provided in the results output file:


These are the columns that are on the file… I expected to obtain results on the fold change of each of the treated samples in relation to the control sample. Could you please help me to get the fold change for individual samples?

Hi @Nidheesh_Thadathil

These tools do not output calculations for individual samples directly. Instead, these only run on replicate pools.

REF → FAQ: Extended Help for Differential Expression Analysis Tools

Differential expression tools all require sample count replicates. Rationale from two of the DEseq tool authors.

In this, they explain how to do this with R directly.

You can run R in Galaxy inside an interactive environment. Rstudio is one choice → GTN Materials Search

However, I’m wondering if Limma might provide alternative results that may interest you? This tutorial covers many of the options and seems worth a review if you are interested. The data you have now is probably an appropriate input already (but you can navigate to the prior tutorial, and the downstream one) → Hands-on: 2: RNA-seq counts to genes / Transcriptomics

Hope this helps! :slight_smile:

Thank you @jennaj

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