I have a number of variables being used in the development of a scale. In my survey analysis I've deemed the 'Not applicable' (NA) selections as missing so they are not used in the analysis - other responses are based upon a 5 pt Likert score.

There are 3 separate groups of interest. I'm wondering if I need to modify the cases in Grp 1 somehow to increase the number of valid cases:

Group number / valid cases / missing cases

Grp 1 / 35 / 107

Grp 2 / 171 / 58

Grp 3 / 321 / 81

Only those cases in which all variables were answered, and not including any NA responses, are included in the valid cases count. Of these invalid cases there are about 100 in which there are numerous NA's selected. Of those 100ish, it looks like 85-90% of those individuals with multiple NA's are from Grp 1, with the remaining 10-15% from Grp 2. 

There are about another 25 cases in which there may be 1 or 2 NA's selected.

All in all there are 529 valid cases and 265 missing cases. The respondent needed to have answered all questions contained in the scale and not have responded with a 'Not Applicable'. Does this low valid cases count for Grp 1 pose problems? Bias?

I'm wondering what others have done to account for NA's in survey analysis. Do you acknowledge the low count and proceed with analysis? In my reading I'm generally finding information on how to account for truly missing data - and that's not exactly the case here.

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