Contingency tables with missing values but chi2 with valid values

[Helen Fay]

Hi everyone,
I'am comparing a dichotomic variable between 2 groups. Group n°1 is 199 observations including 2 missing values and Group n°2 is 110 observations including 1 missing value. I want to tabulate percentage based on the hole sample per comparison group so I will have a fix n for each group but present chi square statistics based only on valid values. Does it make sense? I wonder if this correct...If not what alternative do I have?
Thank you

[Hasanin Sanim]

Please clarify with an example.
If this is the situation
Do you smoke cigarettes? Yes / No

Group n1 is Urban - 199 obs with2 missing values
Group n2 is Rural - 110 obs with 110 obs with 1 missing values

group n1 group n2
yes no
no yes
no no
yes yes
no
yes

Is this your questions problem?