I am trying to implement the manual example of 'aroma.affymetrix' package (http://digitalassets.lib.berkeley.edu/sdtr/ucb/text/745.pdf, page 8). I tried to structure my data as requested, thus I have:

The annotation data:
/annotationData/chipTypes/Axiom_MNEc670/Axiom_MNEc670.CDF

/annotationData/chipTypes/Axiom_MNEc670/Axiom_MNEc670_annot.db

The .CEL files:

/rawData/Axiom_Horse/Axiom_MNEc670/SAM1_15123_plate1_H04_20150521_(Axiom_EquineSNP_plate).CEL

/rawData/Axiom_Horse/Axiom_MNEc670/...

Where '...' means other .CEL files in the same folder. Then I used:

cs <- AffymetrixCelSet$byName("Axiom_Horse", chipType="Axiom_MNEc670")

And I got the following error:

Error: Failed to setup a data set for any of 1 data directories located. The following reasons were reported: (1) [affxparser Fusion SDK exception] Failed to parse header of CEL file: rawData/Axiom_Horse/Axiom_MNEc670/SAM1_15123_plate1_H04_20150521_(Axiom_EquineSNP_plate).CEL
(while trying './rawData/Axiom_Horse/Axiom_MNEc670').

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252    LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C                      
[5] LC_TIME=Dutch_Netherlands.1252    

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

other attached packages:
[1] aroma.light_3.0.0       aroma.affymetrix_2.14.0 affxparser_1.42.0       aroma.core_2.14.0       R.devices_2.13.1       
[6] R.filesets_2.9.0        R.utils_2.2.0           R.oo_1.19.0             R.methodsS3_1.7.0      

loaded via a namespace (and not attached):
 [1] matrixStats_0.15.0 codetools_0.2-14   listenv_0.5.0      future_0.9.0       digest_0.6.8       R.huge_0.9.0       PSCBS_0.60.0      
 [8] tools_3.2.3        R.cache_0.12.0     parallel_3.2.3     base64enc_0.1-3    aroma.apd_0.6.0    R.rsp_0.20.0       globals_0.6.0     
[15] DNAcopy_1.44.0    

Some idea to deal with that?

Hi.  Unfortunately, none of the Affymetrix Axiom chip types are supported by aroma.affymetrix.  This is because Axiom is quite a different assay/technology.  Leaving aside that I don't know which of the traditional Affymetrix preprocessing methods would work on this type of data, the absolute first issue is to be able to parse these Axiom CEL files.  All parsing of Affymetrix data files is done by the affxparser package.  It does indeed support reading of Axiom CDF files, but when it comes to Axiom CEL files it chokes

> library("affxparser")
> hdr <- readCelHeader("NA18500_YRI_Axiom_Exome319.CEL")
Error in readCelHeader("NA18500_YRI_Axiom_Exome319.CEL") :
 [affxparser Fusion SDK exception] Failed to parse header of CEL file: NA18500_YRI_Axiom_Exome319.CEL

This is the same error message that you are seeing when you're trying to access these data via the Aroma Framework.  (BTW, otherwise your Aroma setup looks correct to me).

FYI, I've created affxparser issue 'WISH: Read Axiom CEL files' (https://github.com/HenrikBengtsson/affxparser/issues/20) to have a record of this.  At this point we have no estimate on when or if affxparser will support Axiom CEL files.  It would be a nice start though if it would.