I am trying to process data from Affymetrix HT HG-U133+ PM Array Plate GSE27544 by using affy R package. I am interested to generate the expression values, present/absent calls and p-values. I am using the following code

# read file
file <-  ReadAffy(filenames = file.choose())
eset.mas5 = mas5(file)

# generate expression values
exprSet.nologs = exprs(eset.mas5)

# calls
data.mas5calls = mas5calls(file)
data.mas5calls.calls = exprs(data.mas5calls)
# print(head(data.mas5calls.calls))

# pvalues
pvalue <- assayData(data.mas5calls)[["se.exprs"]]
# print(head(pvalue))

data.full <- cbind(exprSet.nologs, data.mas5calls.calls, pvalue)

But it does not produce expression, which is supposed to done by

# generate expression values
exprSet.nologs = exprs(eset.mas5)

It just gets NA values

 head(exprSet.nologs)
             GSM680176.CEL
1007_PM_s_at            NA
1053_PM_at              NA
117_PM_at               NA
121_PM_at               NA
1255_PM_g_at            NA
1294_PM_at              NA

And when I try to generate calls by

# calls
data.mas5calls = mas5calls(file)

I get  Error in FUN(X[[i]], ...) : NA/NaN/Inf in foreign function call (arg 2)

Which is due to the above NA values. How can I process the data from the above mentioned array.

Please familiarize yourselves a little with the design of the Affymetrix arrays. The design of the HG-U133+ PM array differs from the 'original'  HG-U133 Plus 2.0 array at two points, of which this is the relevant one: "Only perfect match (PM) probes from the cartridge design were retained, while mismatch probes were removed." Source. As a consequence, the P/A calls and MAS5 normalization cannot be performed (because for these the MM probes are also required).

How to proceed? I would go for RMA normalization (which has been repeatedly shown to outperform  MAS5 normalization anyway). Obtaining a P/A (like-)call for the probesets on this array is (AFAIK) not possible.