I'm trying to perform a differential gene expression analysis using some TCGA data that I reprocessed and my data. However I'm worried about the batch effect.
Normally to perform deseq I use this:
dds <- DESeqDataSetFromHTSeqCount(sampleTable = d, directory = directory, design= ~ batch) dds <- estimateSizeFactors(dds) dds <- DESeq(dds)
and then to plot an remove the batch effect I use this:
vsd <- vst(dds) plotPCA(vsd, "batch") assay(vsd) <- limma::removeBatchEffect(assay(vsd), vsd$batch) plotPCA(vsd, "batch")
my doubt is about to perform differential gene expression after removing this batch effect with limma, is there any way? or DeSeq itself do this when I put batch as design?