I am running the workflow "An end to end workflow for differential gene expression using Affymetrix microarrays ".

pData(raw_data) <- pData(raw_data)[, c("Source.Name",
                                       "Characteristics.individual.",
                                       "Factor.Value.disease.",
                                       "Factor.Value.phenotype.")]

exp_raw <- log2(exprs(raw_data))

PCA_raw <- prcomp(t(exp_raw), scale = FALSE)

dataGG <- data.frame(PC1 = PCA_raw$x[,1], PC2 = PCA_raw$x[,2],
                     Disease = pData(raw_data)$Factor.Value.disease.,
                     Phenotype = pData(raw_data)$Factor.Value.phenotype.,
                     Individual = pData(raw_data)$Characteristics.individual.)

arrayQualityMetrics(expressionset = raw_data,
                    outdir = "Report_for_Palmieri_raw",
                    force = TRUE, do.logtransform = TRUE,
                    intgroup = c("Factor.Value.disease.","Factor.Value.phenotype."))

Result:

The directory 'Report_for_Palmieri_raw' has been created.

Error in colnames(pd) %in% intgroup : argument "intgroup" missing，with no default value

What could cause this problem?

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

I'm not sure why this hadn't been detected before, but there seemed to be problem passing the intgroup argument to one of the internal functions.  I've patched this in version arrayQualityMetrics version 3.33.4

This will take a few days to appear in the Bioconductor system, but you can install it now with

BiocInstaller::biocLite('grimbough/arrayQualityMetrics')