proc means data=anne.geno2_good_means0123 noprint;
	class probeuid;
	var genotype2;
	output out=count_freqs;
run;

data count_freqs2;
set count_freqs;
	where _type_=1 and _stat_="N";
run;

data missing_flag;
set count_freqs2;
	if genotype2 ne 52 then missing=1;
		else missing=0;
	drop _type_ _freq_ _stat_;
run;

proc freq data=missing_flag;
	table missing;
run;
*3664 probes are missing at least one obs;

data missing_results;
merge missing_flag anne.results_all_geno2_all0123;
	by probeuid;
run;

proc freq data=missing_results;
	tables missing*norm_flag_log10_bgsub;
run;

data sig_norm_prob;
set anne.results_all_geno2_all0123;
	where fdr_pgenotype2_log10 ne "tan"
		and norm_flag_log10_bgsub =1;
run;
*97 probes are significant and have a normality
problem for ANOVA including line 78;

data sig_norm_prob_no78;
set anne.results_all_geno2_all0123;
	where fdr_pgenotype2_log10_no78 ne "tan"
		and norm_flag_log10_bgsub_no78 =1;
run;
*28 probes are significant and have a normality
problem for ANOVA without line 78;