How to use the Combat-seq for batch effect removal?
2 answers
should i normalized the RNA-seq raw countdata before or after using the Combat-seq?
Please see in this post below which had been discussed earlier.
In Which Order Use Normalization And Batch Effects Removal?
Also remember that standard methods like DESeq2, edgeR etc. can handle batch effect very well. You do not have to perform batch correction using outside softwares if you are planning to perform differential expression analysis using these methods.
Thank you~!:)
Can I handle the batch effect in this manner?
dds.dex <- DESeqDataSetFromMatrix(countData = round(ga.ta.dex.merge), colData = coldata, design = ~ condition)
dds.dex <- DESeq(dds.dex)
vsd <- vst(dds.dex, blind=FALSE)
mat <- assay(vsd)
mm <- model.matrix(~condition, colData(vsd))
mat <- limma::removeBatchEffect(mat, batch=vsd$batch , design=mm)
assay(vsd) <- mat
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Thank you so much~!!:)