Entering edit mode
21 months ago
biotrekker
▴
110
Hello I am trying to use edgeR's filterbyExpr
with DESeq2. I am running into an issue where I cannot use filterByExpr
with DESeq2, unless I do not specify keep.lib.sizes = FALSE (which is recommended by edgeR) how do I use filterByExpr
on my DESeqDataSet
object.
dds <- DESeqDataSetFromTximport(txi=txi.kallisto.tsv, colData=meta, design= ~1)
# Filter by expression (Get rid of low variance )
keep.exprs <- filterByExpr(dds)
dds_pre_filt<- dds[keep.exprs,]
dim(dds_pre_filt)
dds_deseq <- DESeq(dds_pre_filt) #
norm_dds<-vst(dds_deseq) # vst normalization
What I want is to be able to to is:
dds_pre_filt<- dds[keep.exprs,, keep.lib.sizes = FALSE]
and then precede with normalization