Question: Could the batch effect be a set of numeric values in DEseq2?
0
gravatar for Cecelia
9 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 • 253 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by Cecelia20
1
gravatar for Devon Ryan
9 months ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k 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 9 months ago by Devon Ryan91k

Thanks Devon. Your comments are always helpful!

ADD REPLYlink written 9 months ago by Cecelia20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1551 users visited in the last hour