Hi there!

I am trying to perform a gene set enrichment analysis with qusage package in order to incorporate one random effect. I am comparing two groups of patients on one contrast (which is basically my only fixed effect in my design) and I have multiple samples per patient (which is my random effect).

This is my code:

# First I uploaded (1) all Genesets from the MSigDB/Broadway institue, (2) my logcpm matrix constructed with edgeR/limma and (3) my design
library(qusage)
library(nlme)
eset <- top500logcpm
fixedeffects <- Design$SVZstatus
# contrast factor 
con.fac <- Design$SVZstatus
contrast = "SVZ - nonSVZ"
sampleID <- Design$Name
subject <- Design$Subject
qusage.result.random<-qgen(eset, Design,
                            fixed=fixedeffects,
                            contrast.factor=fixedeffects,
                            contrast=contrast,
                            geneSets=geneSets,
                            random=subject,
                            design.sampleid="sampleID")

Unfortunately, I get this error:

Error in `[.data.frame`(design, , design.sampleid) : 
  undefined columns selected

I checked my column names in my design, but there are no typo's... What am I doing wrong? Your help is appreciated!

I have found a solution: it is sufficient to provide the column name of the design (so in my case: fixedeffects <- ~SVZstatus instead of fixedeffects <- Design$SVZstatus). Now it works. :)