Occasionally, you may notice an apparent aberration regarding Advanced Filtering of SNPs, or filtering-based statistics such as Fisher's Exact Text SNP Search or Odds Ratio SNP Search. The reason for this is that ArrayStar places SNPs which do not affirmatively match the filtering criteria in the "not matching" conceptual category. This conceptual category contains the SNPs not displayed as results in the filtering, nor placed in the first column of the contingency table.
When a filter like "No splice" is performed, for example, there are internally three kinds of entries: "Splice", "No splice", and "Other." "Other" entries are typically samples where no SNP (and therefore, no splice) was found. As you can see in the table below, "Other" is placed in the "Not matching" conceptual category both when you filter for "Splice" as well as when you filter for "No splice." Any perceived irregularities are likely due to this overlap phenomenon.
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Example 1 |
Example 2 | |
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Filter for > |
"Splice" |
"No Splice" |
"Non-synonymous AND Pnotref >= 90%" |
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Matching |
Splice |
No splice |
SNPs which are both Non-synonymous AND Pnotref >= 90% |
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Not Matching |
No splice, other |
Splice, other |
SNPs which are Non-synonymous with Pnotref < 90% SNPs which are Synonymous regardless of Pnotref SNPs which are not in a coding region regardless of Pnotref SNPs which are in a project with no feature information regardless of Pnotref Entries which are not called as SNPs |