Refresh DEseq2R script

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Revision as of 19:35, 27 July 2022 by Joseph (talk | contribs) (Created page with "==Introduction== If your users ran an RNA-seq DEseq2 analysis using DEseq2R, between April 2021 and March 2022, it is important that you update the R integration script and re...")
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Introduction

If your users ran an RNA-seq DEseq2 analysis using DEseq2R, between April 2021 and March 2022, it is important that you update the R integration script and rerun the analysis to ensure full accuracy.

Starting in OmicSoft Suite version 11.3, users can choose to run DEseq2 analysis either using the legacy DEseq2 pipeline (C# implementation of DEseq2 v1.10) or the new DEseq2 v1.30, directly launching analyses in your R environment.

In the new integration between OmicSoft Suite and R-based DEseq2 v1.30, differences in default sort order ("lexicographical" vs "ASCII" ordering) resulted in a small percentage of statistical comparisons to flip case and control samples; in certain very complex models additional effects can be observed.

To fix the issue, simply delete the file "DEseq2R.txt"; the next time you run a DEseq2 analysis the updated script will be downloaded.

Refresh DEseq2R for OmicSoft Studio

  1. . Navigate to your Omicsoft folder (default: Documents/Omicsoft)
  2. . Navigate to the Rscripts subfolder
  3. . Delete "DEseq2.txt"

Refresh DEseq2R for OmicSoft Server (Windows)

  1. . Navigate to your server's Omicsoft folder
    1. . Set in ArrayServer.cfg with OmicsoftDirectory
    2. . If not set, it will be a subfolder of BaseDirectory
    3. . If BaseDir is not set, default location is C:\OmicsoftHome\Omicsoft
  2. . Navigate to the Rscripts subfolder
  3. . Delete "DEseq2.txt"

Refresh DEseq2R for OmicSoft Server (Linux)

  1. . Navigate to your server's Omicsoft folder
    1. . Set in ArrayServer.cfg with OmicsoftDirectory
    2. . If not set, it will be a subfolder of BaseDirectory
  2. . Navigate to the Rscripts subfolder
  3. . Delete "DEseq2.txt"