I am working on RNA-Seq data. I'm using DESeq2 for my analysis. I have 20 samples from 3 batches. I am testing for 2 conditions, cond1 and cond2.
dds<-DESeqDataSetFromMatrix(countData=countTable3,colData=coldata,design = ~cond1*cond2)
When i performed PCA, I could clearly see some batch effect. I read in the forum that adding batch to the design in DESeq removes the batch effect. But I am not sure if this is the right way to go about it because I can still see the same batch effect
dds<-DESeqDataSetFromMatrix(countData=countTable3,colData=coldata,design = ~batch+cond1*cond2)
I tried using Combat but I'm unable to use combat results in DESeq. It gives me the following error.
Error in DESeqDataSet(se, design = design, ignoreRank) :
some values in assay are negative
I am not sure if removeBatchEffects() function can be used with DESeq. Can someone please help me out here.