How To Understand The Value For The Affychip Of Genomewidesnp_6?

Question

[jlshi.nudt]

I've download a dataset generated by Affymetrix Genome-Wide Human SNP 6.0 Array. I don't understand the means of numbers in series matrix files. The head of the file looks like:

Sample_title Sample1 Sample2 ....

SNP_A-1780270 18 90...

The first row is the samples, and the first column is the ID of each SNP probe. But what the numbers "18, 90" mean? Are these the number of SNPs for each corresponding sample? Thank you.

[Neilfws]

Would help to link to the dataset (assuming it's public) so we can see the data for ourselves.

Answer 1

[Devon Ryan]

The short answer, is that you'll have to check an individual sample from that dataset in GEO (I assume you got the dataset there). The series matrix file just copies whatever's in the the "value" field of the individual samples into a single file. However, that "value" column can have just about anything in it. I just click on a few samples and found genotype (AA,BB, etc.) in one, B allele frequency in a second, and "inferred copy number" in a third.