Question: after I use sva package to remove batch effect,can I use DESeq2 to make DE analysis?
0
gravatar for Ada
2.9 years ago by
Ada0
Ada0 wrote:

hello,here my question. If I use sva packages to remove the batch effect,which mean I need to normalize the read counts.But I want to make DE analysis with DESeq2 ,and that need raw read counts without normalization.and here the conflict is that I need to remove batch effect before differential expression analysis.How can I solve this problem ? I need your help .

rna-seq • 1.6k views
ADD COMMENTlink modified 2.9 years ago by Devon Ryan92k • written 2.9 years ago by Ada0
0
gravatar for Devon Ryan
2.9 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

Please have a read through this bioconductor workflow. It shows your exact use case of combining SVA with DESeq2. The short answer from that is that you should incorporate the output from SVA in the model matrix and leave the counts untouched.

ADD COMMENTlink written 2.9 years ago by Devon Ryan92k

Thank you very much!

ADD REPLYlink written 2.9 years ago by Ada0
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