Abi genotyping minimum thresholds - (Jul/21/2006 )
Hi,
I am working in conjunjunction with another postdoc who uses genotyping to determine the end point of our joint experiment.
It is a while since I did any genotyping, and I used a gel based system rather than capilliary but assume that data analysis hasnt changed that much in the past 4 years!
I remember that the group I worked for would disregard any peaks that fell below a minimum threshold level on the fluorescence output (Y axis) to eliminate the possibility of background noise being counted as a real peak. I seem to remember that we disregarded any data where the Y-axis reading was less than 100, with ideal samples showing readings of 2-500. However, my colleague fiddles with the data output, altering the Y axis until peaks can be seen in all samples regardless of the Y-axis reading and is saying that peaks that read under 50 are still real data.
So...my question is, is there an acceptable cut off point, below which data cant be assumed to be real, and if so what value do you use to determine data over background?
thanks!
I am working in conjunjunction with another postdoc who uses genotyping to determine the end point of our joint experiment.
It is a while since I did any genotyping, and I used a gel based system rather than capilliary but assume that data analysis hasnt changed that much in the past 4 years!
I remember that the group I worked for would disregard any peaks that fell below a minimum threshold level on the fluorescence output (Y axis) to eliminate the possibility of background noise being counted as a real peak. I seem to remember that we disregarded any data where the Y-axis reading was less than 100, with ideal samples showing readings of 2-500. However, my colleague fiddles with the data output, altering the Y axis until peaks can be seen in all samples regardless of the Y-axis reading and is saying that peaks that read under 50 are still real data.
So...my question is, is there an acceptable cut off point, below which data cant be assumed to be real, and if so what value do you use to determine data over background?
thanks!
What method do you use for genotyping?
There isn't only one methode....
And i don't really understand why you just speak about Y-axis, on my experiments when i use genotyping i need both axis and the value to determine data over background are given by a specific bakground plate i made at least every month to gauge my ABIprism.
But maybe we don't use the same methode, and and we don't have the same tools...
hope you will find answer soon