Question: Could the batch effect be a set of numeric values in DEseq2?
0
gravatar for Cecelia
20 months ago by
Cecelia20
Cecelia20 wrote:

Hello!

I am using Deseq2 to analyze a RNA-seq dataset. One of the potential batch effect contains numeric data, which indicates the wasp load in a host. The coldata looks like this:

X,Time,Treatment,batch
sampe1,Treat1,1
sample2,Treat1,7
sample3,Treat1,23
sampe4,Treat2,4
sample5,Treat2,59
sample6,Treat2,10
sample7,Control,0
sample8,Control,0
sample9,Control,0

Does Deseq2 also handle numeric conditions or one must convert the wasp load into different levels of factors? It will be very much appreciated if anyone can help!

Cheers, C

rna-seq design deseq2 • 412 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by Cecelia20
1
gravatar for Devon Ryan
20 months ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

DESeq2 and similar programs are perfectly happy with covariates (i.e., numeric values associated with colData). Just note that if you do this with a batch effect then the value associated is expected to have a linear effect...which is probably not the case for actual batches.

ADD COMMENTlink written 20 months ago by Devon Ryan95k

Thanks Devon. Your comments are always helpful!

ADD REPLYlink written 20 months ago by Cecelia20
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