I am working with gene expression data from a RNASeq dataset using DESEq2.
I have realised my housekeeping gene (gene which is expected to be maintained across samples independent of condition) is significantly different between two of my condition groups. Therefore, I would like to normalise all my data to the expression of this gene.
Can I approach it like this?
dds <- DESeq(dds) dds<- estimateSizeFactors(dds, controlGenes=OG_90) dds <- nbinomWaldTest(dds)
I get the following error when running the estimateFactor:
Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, : object 'OG_90' not found
How can I refer to the housekeeping gene in that function?