Since you have 6 diseases with two treatments of each disease, I think that the analysis of covariance is suitable.
The analysis of covariance is a variant of ANOVA. Analysis of covariance allows the researcher to control or adjust for variables that correlate with the dependent variable before comparing the means on the dependent variable. These variables are known as covariates of the dependent variable.
To the extent that the levels of the covariates are different for the different research conditions, unless you adjust your dependent variable for the covariates you will confuse the effects of your independent variables with the influence of the pre-existing differences between the conditions caused by different levels of the covariates.
By controlling for the covariates, essentially you are taking their effect away from your scores on the dependent variable. Thus having adjusted for the covariates, the remaining variation between conditions cannot be due to the covariates.
One common use of ANCOVA is in pre-test/post-test designs. Assume that the pre-test suggests that the different conditions of the experiment have different means prior to testing (e.g. the experimental and control groups are different), ANCOVA may be used to adjust for these pre-test differences.