Batch factor correction in DeSeq2

usegalaxy.org support
1

Hi everyone,
I initially had a bioinformatician run RUVseq in R to generate a tabular file containing corrections for unwanted variation (K=4; denoted as W1 through 4) . I am attempting to supply this file into the DeSeq2 module for DEG analysis.
My tabular file contains the following column entries (6 columns): Sample ID - Groups (e.g. control or treatment) - W1 - W2 - W3 -W4
I keep getting error messages when I run DeSeq2. Is there anything wrong with the format of this tabular file?
Also, do I have to declare this file as a “Single Dataset”; “Multiple dataset.” Not really sure whether that’s relevant here despite being in the choices.
Lastly, should I retain the header info in the tabular file that I upload into galaxy?

I am not a bioinformatician so will appreciate some pearls of wisdom. Thanks.

2

anyone knows what the input file should look like and also do we have to add any identifiers???

thank you in advance…

3

Welcome, @BLESSY_KIRUBA

Example Bioconductor tool usage is in these tutorials → Transcriptomics / Tutorial List

Some extra help about getting the reference data and count tables labeled correctly is covered in this guide → FAQ: Extended Help for Differential Expression Analysis Tools

Please give those a try, and if something is still going wrong, you can share more details about your work and someone here will try to help more. How to share your work is in the banner of the forum or see here directly → How to get faster help with your question

Let’s start there :slight_smile: