DESEQ2 several samples per individual
1
0
Entering edit mode
Bine ▴ 40
@bine-23912
Last seen 3 months 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 • 928 views
ADD COMMENT
1
Entering edit mode
ATpoint ★ 4.0k
@atpoint-13662
Last seen 3 hours ago
Germany

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.

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode

No, we don't have plans to support random effects / correlations _within_ condition group. Blocking across condition is of course covered by including fixed effects in the regression.

ADD REPLY

Login before adding your answer.

Traffic: 750 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6