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Based on genomic position, a total of 107,896 SNP were shared between the 2 platforms; however, based on genotype concordance, only 96,031 SNP had complete concordance at these loci.
There were 1575 rows (679 neurons, 2 platforms from the 2 platform task and 217 neurons from the one platform task) and 2 columns (texture and reward location).
We considered a variant as real if it was validated by Sanger or, in absence of Sanger validation, if it was found in at least one platform and previously annotated, or independently present in at least 2 platforms and not annotated.
Also, the sensitivity to detect CNA by the 2 platforms was compared.
We found that Affymetrix yielded a slightly higher overall score compared with the other 2 platforms.
Another reason for the low concordance between the 2 platforms may be their differences in sensitivity.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com