Differential Expression Analysis-Input is DESeq Standardized
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sushimoto • 0
@2fc02fda
Last seen 10 weeks ago
Turkey

Hello, this is my 3rd question in a week. Sorry about that.

1) So it seems like I have finally found data to do differentially expression analysis. So my question is, can I do DESeq2 differential expression analysis of the data from this link: https://xenabrowser.net/datapages/?dataset=TCGA-GTEx-TARGET-gene-exp-counts.deseq2-normalized.log2&host=https%3A%2F%2Ftoil.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.

2) If I can, should I skip the normalization?

3) If I cannot, in this link (https://xenabrowser.net/datapages/?cohort=TCGA%20TARGET%20GTEx&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443) which "gene expression RNAseq" dataset would be suitable for DEG analysis?

Thanks in advance.

rnaseq RNASeqData limma limmaGUI • 150 views
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@mikelove
Last seen 2 days ago
United States

These aren’t really appropriate questions for software developers in my opinion, this is requesting pointers for how to approach an analysis, asking for developers to do work for you. I’d recommend posting on Biostars. The Bioconductor support site is specifically for support from software developers on how to use their software.

The question about using pre-scaled data with DESeq2 has been answered numerous times in the past here (no, you should not).

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