topic Re: Pooled analysis for sensitivity and specificity in Statistical Procedures

Pooled analysis for sensitivity and specificity

J_Park — Wed, 08 Jan 2025 17:57:00 GMT

I tried to use proc glimmix for the pooled analysis but I kept getting error about "solution." What is wrong with my sas code? Thank you for your help!

data meta_analysis_data;
input study_id sensitivity specificity se_sensitivity se_specificity;
datalines;
1 0.85 0.75 0.05 0.04
2 0.90 0.80 0.04 0.03
3 0.80 0.77 0.06 0.05
4 0.88 0.82 0.05 0.04
;
run;

data logit_data;
set meta_analysis_data;
logit_sensitivity = log(sensitivity / (1 - sensitivity));
logit_specificity = log(specificity / (1 - specificity));
run;

proc means data=logit_data nmiss;
var logit_sensitivity logit_specificity;
run;

proc freq data=logit_data;
tables logit_sensitivity*logit_specificity / missing;
run;

proc glimmix data=logit_data method=laplace;
class study_id;

/* Fit the model for logit_sensitivity only */
model logit_sensitivity = / solution dist=normal link=identity;

/* Random intercept for each study */
random study_id / subject=study_id type=vc;

ods output solution=sensitivity_results;
run;

proc print data=sensitivity_results;
run;

Re: Pooled analysis for sensitivity and specificity

SteveDenham — Wed, 08 Jan 2025 18:52:47 GMT

Consider changing the last RANDOM statement to:

random  intercept/subject=study_id;

Having study_id as both the random effect and the subject of the random effect most likely is the source of your error.

SteveDenham

Re: Pooled analysis for sensitivity and specificity

SteveDenham — Wed, 08 Jan 2025 18:58:10 GMT

One other change - the SOLUTION is output to the ODS file ParameterEstimates, so try this (which ran without errors or warnings for me)

data meta_analysis_data;
input study_id sensitivity specificity se_sensitivity se_specificity;
datalines;
1 0.85 0.75 0.05 0.04
2 0.90 0.80 0.04 0.03
3 0.80 0.77 0.06 0.05
4 0.88 0.82 0.05 0.04
;
run;

data logit_data;
set meta_analysis_data;
logit_sensitivity = log(sensitivity / (1 - sensitivity));
logit_specificity = log(specificity / (1 - specificity));
run;

proc means data=logit_data nmiss;
var logit_sensitivity logit_specificity;
run;

proc freq data=logit_data;
tables logit_sensitivity*logit_specificity / missing;
run;

proc glimmix data=logit_data method=laplace;
class study_id;

/* Fit the model for logit_sensitivity only */
model logit_sensitivity = / solution dist=normal link=identity;

/* Random intercept for each study */
random intercept / subject=study_id type=vc;

ods output parameterestimates=sensitivity_results;
run;

proc print data=sensitivity_results;
run;

SteveDenham

Re: Pooled analysis for sensitivity and specificity

J_Park — Wed, 08 Jan 2025 21:05:33 GMT

Thank you so much for your solution! It ran without any errors. Now my question is what this random intercept for sensitivity (=1.83, stdErr = 0.15, p = 0.0012) mean. This is my first try to use this method to do a pooled analysis. I was expecting to see the pooled sensitivity. Any advice would be greatly appreciated.

Re: Pooled analysis for sensitivity and specificity

Ksharp — Thu, 09 Jan 2025 01:52:22 GMT

It looks like you are doing Meta Analysis.

Here random intercept for sensitivity is ODDS Ratio if you EXP() it .

a.k.a

exp(1.83)= odds ratio = sensitivity/(1-sensitivity)

https://support.sas.com/kb/24/170.html

Re: Pooled analysis for sensitivity and specificity

J_Park — Thu, 09 Jan 2025 02:14:41 GMT

Thank you so much for the suggestion and also the SAS document! I will read it carefully and see how I can modify my code to get a pooled sensitivity. Thank you!

Re: Pooled analysis for sensitivity and specificity

Ksharp — Thu, 09 Jan 2025 02:29:24 GMT

sensitivity or specificity are just binomial distribution ratio.

You can Pooled them if you have their std error by PROC MIANALYSIS.

Here is an example for pooled sensitivity .

data meta_analysis_data;
input study_id sensitivity specificity se_sensitivity se_specificity;
datalines;
1 0.85 0.75 0.05 0.04
2 0.90 0.80 0.04 0.03
3 0.80 0.77 0.06 0.05
4 0.88 0.82 0.05 0.04
;
run;
data have;
 set meta_analysis_data;
 level=1;count=100*sensitivity;output;
 level=0;count=100*(1-sensitivity);output;
 keep study_id level count;
run;
ods select none;
proc freq data=have;
by study_id;
table level/binomial(level='1' cl=exact);
weight count;
ods output  Binomial= Binomial;
run;
ods select all;
proc transpose data= Binomial out= Binomial2;
by study_id;
var nvalue1;
id name1;
run;

proc mianalyze data=Binomial2;
  modeleffects _BIN_;
  stderr E_BIN;
run;

Re: Pooled analysis for sensitivity and specificity

J_Park — Thu, 09 Jan 2025 02:40:39 GMT

This is great! Thank you so much for your advice!!!