The PSMOOTH Procedure

Example 9.1 Displaying Plot of PROC PSMOOTH Output Data Set

Data other than the output data sets from the CASECONTROL and FAMILY procedures can be used in PROC PSMOOTH; here is an example of how to use $p$ -values from another source, read into a SAS data set by using the following DATA step.

data tests;
   input Marker Pvalue @@;
   datalines;
 1  0.72841     2   0.40271
 3  0.32147     4   0.91616
 5  0.27377     6   0.48943
 7  0.40131     8   0.25555
 9  0.57585    10   0.20925
11  0.01531    12   0.23306
13  0.69397    14   0.33040
15  0.97265    16   0.53639
17  0.88397    18   0.03188
19  0.13570    20   0.79138
21  0.99467    22   0.37831
23  0.86459    24   0.97092
25  0.19372    26   0.85339
27  0.32078    28   0.31806
29  0.00655    30   0.82401
31  0.65339    32   0.36115
33  0.92704    34   0.49558
35  0.64842    36   0.43606
37  0.67060    38   0.87520
39  0.78006    40   0.27252
41  0.28561    42   0.80495
43  0.98159    44   0.97030
45  0.53831    46   0.78712
47  0.88493    48   0.36260
49  0.53310    50   0.65709
51  0.26527    52   0.46860
53  0.55465    54   0.54956
55  0.44477    56   0.04933
57  0.12016    58   0.76181
59  0.80158    60   0.18244
61  0.01382    62   0.15100
63  0.04713    64   0.52655
65  0.59368    66   0.94420
67  0.60104    68   0.32848
69  0.90195    70   0.21374
71  0.95471    72   0.14145
73  0.95215    74   0.70330
75  0.19921    76   0.99086
77  0.75736    78   0.23761
79  0.87260    80   0.91472
81  0.33650    82   0.26160
83  0.41948    84   0.62817
85  0.48721    86   0.67093
87  0.53089    88   0.13623
89  0.44344    90   0.41172
;

The following code applies Simes’ method for multiple hypothesis testing in order to adjust the $p$ -values.

proc psmooth data=tests out=pnew simes bandwidth=3 to 9 by 2 neglog;
   var Pvalue;
   id Marker;
run;

proc sgplot data=pnew;
   series x=Marker y=Pvalue    / lineattrs=(pattern=solid);
   series x=Marker y=Pvalue_S3 / lineattrs=(pattern=solid);
   series x=Marker y=Pvalue_S5 / lineattrs=(pattern=solid);
   series x=Marker y=Pvalue_S7 / lineattrs=(pattern=solid);
   series x=Marker y=Pvalue_S9 / lineattrs=(pattern=solid);
   refline 3.0 / axis=y;
   discretelegend;
run;

The NEGLOG option is used in the PROC PSMOOTH statement to facilitate plotting the $p$ -values by using the GPLOT procedure of SAS/GRAPH. The plot in Output 9.1.1 demonstrates the effect of the different window sizes that are implemented.

Output 9.1.1: Line Plot of Negative Log $p$ -Values

Note how the plots become progressively smoother as the window size increases. Points above the horizontal reference line represent significant $p$ -values at the 0.05 level. While six of the markers have significant $p$ -values before adjustment, only the method that uses a bandwidth of 3 finds any significant markers, all in the 26–32 region. This can be an indication that the other five markers are significant only by chance; that is, they might be false positives.