Question: batch effect Deseq2 Wald test
0
gravatar for mariannapauletto
13 months ago by
mariannapauletto20 wrote:

Hi all,

I'm using Deseq2 to analyze a set of data with a relevant batch effect related to the library preparation day. I used the LR test and added the batch effect. It worked but I'd like to have comparisons between the specific conditions.

Is it possible to use the Wald test while controlling a batch effect??

Thank you for your time and support!

Best Marianna

batch rna-seq wald test deseq2 • 438 views
ADD COMMENTlink modified 13 months ago by Devon Ryan94k • written 13 months ago by mariannapauletto20
0
gravatar for Devon Ryan
13 months ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

Yes, a Wald test is quite flexible (it's usually easier to deal with than an LRT) and you can use it by not specifying LRT in DESeq2 (the default is a Wald test).

ADD COMMENTlink written 13 months ago by Devon Ryan94k

Thank you Davon Ryan,

So to control for batch effect and perform a Wal test I should use the following approach

dds <- DESeqDataSetFromMatrix(countData = cts,
                              colData = coldata,
                              design = ~ batch + condition)

dds <- DESeq(dds, reduced=~batch)

Is it correct?

Thank you!

Best

Marianna

ADD REPLYlink modified 13 months ago • written 13 months ago by mariannapauletto20

You don't need reduced=~batch, since there's no reduced model used.

ADD REPLYlink written 13 months ago by Devon Ryan94k

Ok, so with the Wald test you cannot control the batch effect. Isn't it?

Marianna

ADD REPLYlink written 13 months ago by mariannapauletto20

I'm not sure how you got that interpretation, you control it by adding it to your model, just as in an LRT.

ADD REPLYlink written 13 months ago by Devon Ryan94k

Thank you Devon Ryan

ADD REPLYlink written 13 months ago by mariannapauletto20
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