Hi, please specify which tool and expression in it I can use to obtain LogFC from Log2(FC) (column 3) in my “Annotated DESeq2 results” file, resulted from Reference-based RNA-Seq data analysis. The general idea is to perform Volcano plot based on “Visualization of RNA-Seq results with Volcano Plot” tutorial. In that training “limma-voom_luminalpregnant-luminallactate” dataset I see logFC. In “Annotated DESeq2 results” dataset Log2(FC). I used “Compute on rows (Galaxy Version 2.1)” tool with expression - sign(с3-1)*с3, where c3 is a column in “Annotated DESeq2 results” dataset with Log2(FC) and got error.
Thank you in advance
You can use the output you have with the tutorial. That would make use of the statistics calculated by DESeq2. Hands-on: Visualization of RNA-Seq results with Volcano Plot / Visualization of RNA-Seq results with Volcano Plot / Transcriptomics
If you want to obtain the other values, get your count files from the prior tutorial, and process with Limma instead. Why? The Compute tool cannot replace any of these tools: DESeq2, EdgeR, Limma.
How to reuse the count files
The count files from the tutorial you are currently following are produced at this step. → https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#counting-the-number-of-reads-per-annotated-gene.
You can then start with the Transcriptomics End-to-End tutorial – Step 2. Your count files will be individual dataset files instead of a count matrix as described in the tutorial, but that is fine – the tool can be used either way. See here → Transcriptomics / Tutorial List then here directly → Hands-on: 2: RNA-seq counts to genes / 2: RNA-seq counts to genes / Transcriptomics
Be sure to carry over your count files and your reference data! If you want to create a count matrix, you can back up to Step 1 in that same series. See → Hands-on: 1: RNA-Seq reads to counts / 1: RNA-Seq reads to counts / Transcriptomics
The output from the Step 2 tutorial is the same as was used in this Volcano plot tutorial here. → Hands-on: Visualization of RNA-Seq results with Volcano Plot / Visualization of RNA-Seq results with Volcano Plot / Transcriptomics
Hopefully this helps! 
Dear jennaj, by saying “you can use the output you have with the tutorial” you mean that the c3 column is correct to build Volcano?
Sure, you can try that.
Then if you want to replicate the results in the other tutorial, you can run your count files through Limma and do it that way. Maybe compare to see if you can understand why those are different.