Quality_control_snpchip_analysis_50K_96K

Question

[tvibhaps]

Hi there, I am trying to perform quality control of our SNPchip data (.CEL files) but my DQC script is unable to read .cdf file what i understood so far and throws the error as below- *

Loading options from file: my_pwd/Analysis/Axiom_NAAS_50K.r1.apt-geno-qc.AxiomQC1.xml
 cdf-file = Axiom_NAAS_50K.r1.cdf
 target-sketch = Axiom_NAAS_50K.r1.AxiomGT1.sketch
 qcc-file = Axiom_NAAS_50K.r1.qcc
 qca-file = Axiom_NAAS_50K.r1.qca
 female-thresh = 0.54
 male-thresh = 1.0
*
Read 5624 cel files from: cel_list1.txt
Checking chip type on all cel files.

**FATAL ERROR:EngineUtil::getCdfChipType(**) - Can't read header for '**Axiom_NAAS_50K.r1.cdf'**. Description: Unable to open the file.

I don't see any .cdf file in my Analysis folder.

Should i re-download the Analysis folder? If yes, from where i should get the direct download link of Axiom analysis software? I am trying to get it (found the thermofisher/Affymetrix_Software/ page and manual as well) but unsuccessful so far for direct download link. Thanks in advance.

Answer 1

[tvibhaps]

Solved it!!

[GenoMax]

Please post the actual solution so it is useful for someone who happens to find this post via search in future. If this was due to user error then consider deleting this thread since it provides no useful information.