Question: Error aroma.affymetrix [affxparser Fusion SDK exception]
0
gravatar for Vinicius Henrique da Silva
3.7 years ago by
Brazil

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?

affxparser affymetrix • 912 views
ADD COMMENTlink modified 3.7 years ago by Henrik Bengtsson2.4k • written 3.7 years ago by Vinicius Henrique da Silva40
Answer: Error aroma.affymetrix [affxparser Fusion SDK exception]
3
gravatar for Henrik Bengtsson
3.7 years ago by
United States
Henrik Bengtsson2.4k wrote:

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.

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Henrik Bengtsson2.4k

Thank you for your clarifications Henrik! 
I am just wondering if I could convert the Axiom .CEL files to a format which is readable by aroma.affymetrix?
I tried 'convertCel()' but I just got a core dump error.

ADD REPLYlink written 3.7 years ago by Vinicius Henrique da Silva40

Unfortunately, there is no simple workaround allowing Axiom CEL files to be processed.  FYI, convertCel() would need to read the CEL files and that's the where the first problem lies.

BTW, when you say you get a "core dump error" when you use convertCel(), do you really mean that R core dumps and aborts?  If so, that's a bug and should not happen.  If just a regular error, then ok.

ADD REPLYlink written 3.7 years ago by Henrik Bengtsson2.4k

The R crashes after shows the error. Thus, may it is a bug.  

ADD REPLYlink written 3.7 years ago by Vinicius Henrique da Silva40

Would you mind sharing all of your commands exactly as you use them for it to crash so I/we can try to reproduce it.

ADD REPLYlink written 3.7 years ago by Henrik Bengtsson2.4k
> convertCel("SAM1_plate2_B07_Axiom_EquineSNP_plate_.CEL", "test.CEL")
terminate called after throwing an instance of 'affymetrix_calvin_exceptions::DataGroupNotFoundException'
Aborted (core dumped)

 

ADD REPLYlink written 3.7 years ago by Vinicius Henrique da Silva40

Hmm... I cannot reproduce this with the few Axiom CEL files I have (different chip type).  Would you mind making the problematic CEL file available for download to us so we can reproduce the problem?  You can email the download link to me at henrikb@braju.com.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Henrik Bengtsson2.4k

Please, do you know how to solve this?

>convertCel(pathname,outputname, readMap=NULL, writeMap=NULL, version="4",newChipType=NULL,.validate=FALSE, verbose=FALSE)
Error in readCelHeader(filename) :
  [affxparser Fusion SDK exception] Failed to parse header of CEL file: /home/bioevo/Desktop/celfile/DEF3.CEL

I'm working with an Axiom Human Origins Array. I need to normalize the data.

Thanks

ADD REPLYlink written 3.2 years ago by Bag_80
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