Question

How to make DGEList and design matrix by edgeR package

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prity6459 • 0

@84d63c4c

Last seen 6 months ago

France

Hi,

I have 6 samples/ groups with 3 replicates (In total 17; one sample contains 2 replicates). the sample names are Mf, Bf, Ef, Mr, Br, and Er. Suppose Mf, Bf, and Ef are coming from control and Mr, Br, and Er are coming from treatment.

How to make DGEList and design matrix for that. I want to get DEGs (differentially expressed genes) between Mr-Mf, Br-Bf, Er-Ef.

Thank you in advance for your input.

DGEList edgeR • 365 views

ADD COMMENT • link 6 months ago prity6459 • 0

score 0 · Answer 1 · 2024-04-19

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Gordon Smyth 51k

@gordon-smyth

Last seen 1 hour ago

WEHI, Melbourne, Australia

Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago.

Please have a read of the edgeR User's Guide.

ADD COMMENT • link 6 months ago Gordon Smyth 51k

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Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making those, as I am new in transcriptomic data analysis.

ADD REPLY • link 6 months ago prity6459 • 0