PROBLEM: When attempting to validate an Illumina Genotyping Processed Matrix SNP data TXT file based on the HumanHap550v3_A design in caArray, you may receive the following error message:
"1 data file(s) are in a format not currently supported for parsing. These files may only be included for validation when validating an SDRF that refers to the files."
SOLUTION: The Illumina SNP data file must be edited before it can be validated by caArray. Specifically, the data table header descriptions in the first row and their corresponding values in the second row must be deleted. An example of this content is shown below:
ID_REF GSM302898 GC_SCORE Theta R B_Allele_Freq Log_R_Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3197343 0.006295365 6.168365 0.0005793257 0.4340365
The revision can be done in any plain text editor such as Windows Notepad. If, after revising the TXT file and attempting to validate it again, you still receive the same error message, check the version of your caArray installation. If you are running v2.3, upgrade to v2.4, then repeat the validation procedure.
