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Question: Matched patient samples in Deseq2
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gravatar for sf533
8 months ago by
sf533 • 20
sf533 • 20 wrote:

Hi,

I wish to use the Deseq2 tool on Galaxy but I am unsure how to incorporate the fact that my samples are matched patient samples before and after treatment.

The primary factor that effects gene expression will be Treatment (before and after).

However I also want to account for the secondary factor that each matched sample (before and after) is from a different patient. I don't know how to input this correctly. Do I have to put each patient as a different factor and enter the before and after treatment samples as factor levels?

Thanks

factor rna-seq deseq2 level • 408 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by sf533 • 20
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gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, this would be one way to run the analysis. Please see the help on the tool form and the linked DeSeq2 documentation for usage examples: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html

Galaxy tutorial examples:

All Galaxy tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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