Whst does the term "call rate" in SNP analysis mean? - (Feb/04/2008 )
hello everyone,
i was reading this paper on a genome wide association study on breast cancer. In methodolgy they excluded certain samples on the basis of "call rate of SNP" and can you give any references online.
thanks
From what I understand a "call" is basically the genotype assignment. I pulled this quote from the background of the paper referenced below (open access paper).
If a SNP's probe intensity values do not pass the detection filter score (DS) or the RAS scores fall outside the boundaries of the statistical model then the SNP is assigned a "NoCall" value. The overall call rate of a sample is equal to the number of SNPs receiving an AA, AB, or BB genotype call divided by the total number of SNPs on the chip.
http://www.biomedcentral.com/1471-2164/6/149
SNiPer: Improved SNP genotype calling for Affymetrix 10K GeneChip microarray data
Matthew J Huentelman*, David W Craig*, Albert D Shieh*, Jason J Corneveaux, Diane Hu-Lince, John V Pearson and Dietrich A Stephan
I hope this was helpful.
If a SNP's probe intensity values do not pass the detection filter score (DS) or the RAS scores fall outside the boundaries of the statistical model then the SNP is assigned a "NoCall" value. The overall call rate of a sample is equal to the number of SNPs receiving an AA, AB, or BB genotype call divided by the total number of SNPs on the chip.
http://www.biomedcentral.com/1471-2164/6/149
SNiPer: Improved SNP genotype calling for Affymetrix 10K GeneChip microarray data
Matthew J Huentelman*, David W Craig*, Albert D Shieh*, Jason J Corneveaux, Diane Hu-Lince, John V Pearson and Dietrich A Stephan
I hope this was helpful.
Thankyou for your prompt reply. i am afraid many of these terms (DS, RAS, SNP probes intensity value) are new to me. can you recommend some basic literature i can read to understand them?
Sorry for the delay in responding - I was not getting notified when there is a response to a post.
Here is a website with some information:
http://www.dorak.info/epi/glosge.html
http://www.dorak.info/epi/genetepi.html - main page for the site
As well as a glossary with genetic epi info:
http://www.upf.edu/cexs/recerca/bioevo/200...afell-JECH3.pdf