error while plot data with deSeq2

error while plot data with deSeq2



I am getting an error while plotting figures after running DESeq2. Here is what I have done:

dds <- DESeqDataSetFromMatrix(countData = mydata, colData = meta, design = ~ Diet)
dds <- estimateSizeFactors(dds)
dds <- DESeq(dds)
plotCounts(dds, gene="ENSSSAG00000003723", intgroup=c("Diet") )

Error in .local(object, ...) : unused argument (intgroup = "Diet")

rld <- rlog(dds, blind=TRUE)
plotPCA(rld, intgroup=c("Diet")) +theme_bw()

Error in .local(object, ...) : unused argument (intgroup = "Diet")

But if I remove intgroup from the code, it works, but I need to look at plot with “Diet” groups

> dds
class: DESeqDataSet 
dim: 42350 48 
metadata(1): version
assays(6): counts mu ... replaceCounts replaceCooks
rownames(42350): ENSSSAG00000004313 ENSSSAG00000047403 ... ENSSSAG00000092601 ENSSSAG00000091009
rowData names(31): baseMean baseVar ... maxCooks replace
colnames(48): T3_mc1_tk2_Lh005 T3_mc1_tk3_Lh001 ... T3_mn3_tk2_Lh001 T3_mn3_tk2_Lh007
colData names(8): id Time ... sizeFactor replaceable




Read more here: Source link