Are there any tutorials available for Nanostring data differential expression analysis using DEseq2 ?

Question

[DareDevil]

I was trying to perform differential expression (DE) analysis for Nanostring using NanoStringDiff but it takes too much time than expected. I came across some paper where they do DE analysis using DESeq2. Are there any such tutorials available for analyzing nanostring data?

Answer 1

[ATpoint]

This is possible according to the developer https://support.bioconductor.org/p/123295/#123296 but you have to make sure not to skew the normalization. Use MA-plots to ensure that the control genes are distributed along y=0 in the plot.

Answer 2

[Thind amarinder]

One GitHub repository, but not Documented well. https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa163/5891144 I am working on it and modifying/writing some R script for Deseq2. When done I will share it on Github and update it here.

If you have technical replicate Better to go with the RUVIII approach, In another case may be UQ+RUVg iterations.

I am updating the R script which is integrating different Packages and Bioconductor packages... details can be found here https://github.com/amarinderthind/Nanostring_normalization_Meta

[DareDevil]

Thanks I have seen this but the steps are not documented well. I will also try to put this in a way of layman language

[Thind amarinder]

https://github.com/amarinderthind/Nanostring_normalization_Meta