I am using PIANO to determine differentially expressed genes. My setup file looks like this:

                           TYPE
CELid1.CEL     CONTROL
CELid2.CEL     CONTROL
CELid3.CEL     TREATMENT
...

my annotation looks like this:

                      SYMBOL     chromosome   start
1007_s_at   DDR1           1                        1
1053_s_at   RFC2           1                        1
...

I am able to run loadMAdata:

loadMAdata(datadir = '/crex1/proj/uppstore2017031/Rui/testCMAP/', setup = mysetup, platform = "NULL", normalization = "rma", annotation = myannot)

I am able to run loadMAdata, but then cannot run diffExp because I get the following error:

Error in factors[i] <- factorAnnot[rownames(arrayData$setup) == colnames(arrayData$dataNorm)[i]] : replacement has length zero

This because extractFactors is missing something. I was looking at the source code of extractFactors, and the factors are not being built in the iteration:

# Get factors from setup
  factorAnnot <- arrayData$setup[,1]
  if(dim(arrayData$setup)[2] > 1) {   ##### HERE
    for(i in 1:(dim(arrayData$setup)[2]-1)) {
      factorAnnot <- paste(factorAnnot,arrayData$setup[,i+1], sep="_")
    }
  }

What am I missing?