I used DEXSeq package to analyze RNA-seq data with two genotypes: KO vs WT, and two treatments: treated vs untreated. I are interested in the interaction between genotype and treatment, i.e. the effects of KO + treated. I preprocessed the data in R using summarizeOverlaps function followed by by DEXSeqDataSetFromSE. I used the following code chunk. Everything worked fine till the last reporting step with DEXSeqHTML. It asked for a column called condition in the sample annotation of DEXSeqDataSet, which I don’t use throughput all analysis. Note that I did get 21 significant exon events as shown in the end.
I used DEXSeq_1.22.0. let me know if the sessionInfo is needed. It looks like DEXSeqHTML function need to be updated. Please help or let me know what can I do? Thank you.
colData(se)$Genotype = samples$Genotype
colData(se)$Treatment = samples$Treatment
dxd = DEXSeqDataSetFromSE(se,
design= ~ sample + exon + Genotype:exon + Treatment:exon + Genotype:Treatment:exon)
dxd = estimateSizeFactors(dxd)
dxd = estimateDispersions(dxd)
dxd = testForDEU(dxd, reducedModel = ~sample + exon + Genotype:exon + Treatment:exon)
dxr1 = DEXSeqResults(dxd)
colors <- brewer.pal(4, "Set2")
DEXSeqHTML(dxr1, FDR=0.1 , color = colors)
>table ( dxr1$padj < 0.1 )
> DEXSeqHTML(dxr1, FDR=0.1 , color = colors)
Error in DEXSeqHTML(dxr1, FDR = 0.1, color = colors) :
The value of the parameter fitExpToVar, 'condition', is not a variable from the annotation of the samples. Please specify a column name of the colData slot of the DEXSeqDataSet object.