DESEQ2 several samples per individual
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Bine ▴ 20
@bine-23912
Last seen 14 hours ago
UK

Good afternoon,

A while ago I asked how to treat 3 samples per individual (ID) in a DESEQ2. It was recommended to use Duplicate Correlation in limma. I wonder how to combine both packages:

I run my DESEQ2 with

dds0 <- DESeqDataSetFromMatrix(countData = cts,
                               colData = colData,
                               design = ~ AGE+ DIAGNOSIS + SEX)

I see that the duplicate correlation is run with

dupcor <- duplicateCorrelation(vobj, design, block=colData$ID)

(https://rdrr.io/bioc/limma/man/dupcor.html).

I struggle to combine both approaches here. Can give me a hint?

Unfortunately, I cannot find any example code online of someone using both approaches together.

Thanks so much, Bine

DESeq2 • 176 views
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There is no combination. If you want to use this function then you are bound to use limma throughout your DE testing. DESeq2 is not compatible here.

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Ok thank you. Do you know by any chance if there is now an option to do this in DESEQ2? Someone told me recently that I could use ID as a block, I cant find anything of it, been searching for a while now.

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This was asked many times before, the developer has suggested to use limma for these types of analysis: DESeq2 handling of replicates

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Yes, i know it was asked many times before. I thought maybe something was developed in the meantime since recently someone told me something as mentioned above. Thanks.

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