Described embodiments provide a method and system for signal compensation in a SERDES communication system that includes monitoring the quality of a data signal after passing through a transmission channel. The quality of the data signal is monitored with at least one of a BER calculation algorithm and a received eye quality monitoring algorithm. Variations in channel length of the transmission channel are compensated for by i) adjusting a length of transmission line delay of the data signal from the transmission channel, ii) comparing the data signal quality with a threshold for the adjusted data signal; and iii) repeating i) and ii) until the data signal quality meets the threshold.