<p>I am analyzing some RNA sequencing data from a collaborator where the effect of some ligands on the transcriptome is being looked at. I am using DESeq2 for my analysis. I am looking to compare each of the ligand treatments vs the DMSO. I have attached the MDS plot with this post. There seems to be a lot of variation between the 3 replicates across all the treatments. Based on this plot, is it worth it to use this data to run a differential expression?</p>
<p>It is also at this link below.
<a href="https://i.sstatic.net/ZXhk5.jpg" rel="nofollow noreferrer">https://i.sstatic.net/ZXhk5.jpg</a></p>

<rna-seq><pca>
Is this RNA seq data good based on the MDS plot
# Is this RNA seq data good based on the MDS plot

(Asked by: username_0 on 2022-05-26)

I am analyzing some RNA sequencing data from a collaborator where the effect of some ligands on the transcriptome is being looked at. I am using DESeq2 for my analysis. I am looking to compare each of the ligand treatments vs the DMSO. I have attached the MDS plot with this post. There seems to be a lot of variation between the 3 replicates across all the treatments. Based on this plot, is it worth it to use this data to run a differential expression?

It is also at this link below.
<https://i.sstatic.net/ZXhk5.jpg>

**Tags:** rna-seq, pca

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## 0 answers

