Hi Anh Phan,

You can assign your “undetermined” samples a Ct of 40. This means, if any at all, the signal of amplification in your reaction appears at the 40th cycle of your PCR reaction. Equal to no amplification :) Then you can perform the relative quantification calculations based on the comparative Ct method of your choice.

You can use the link below for help in calculations.

http://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_5279.pdf

Once you plot your quantification results do not forget then to add an explanation in your figure legend and/or in the methods section on how you have performed the calculations and the presentation of your data.

I hope this helps