Hello Everyone,
I have a few simple questions because I am a bit confused.
On a Genome-Wide Human SNP Array 6.0 there are SNPs and CNV-Probes which can be detected.
For each SNP there are two strands for hybridisation reference and alternative. Each strand has a perfect match of the Locus and a mismatch? (So all in all 4 per Locus?)
If they match on the array they can be detected. The color that gets detected gives an answer if the locus is Homozygous or heterozygous.
So lets say we have the SNP rs2843143, Polymorphism: A/G. Then homozygot means that the probe has G and G on its strands or A and A, right? And heterozygot would mean A and G.
The intensity must be high enough to detect this information. But how can an intensity be detected? I though there is only one strand on the array for matching. If something matched, then it is blocked? What did I miss?
I have a results file from an array.
samp1 samp2 samp3
rs1234 0 1 2
rs2345 2 2 3
rs3456 3 0 3
I understand that 1 means the same as AA, 2 means AB, and 3 means BB. But what does the "0" mean? Just "there was not enough information, so nothing was called"?
I would be very happy about any answer!
Thanks!
