Need help!! My SAS code won't work

[caroline_rg]

Hi!

I am a MSc student and I am having difficulty running my SAS code. I am looking at mammary gland data from pigs. Each variable was measured once. The project has a completely randomized design. 

I am trying to run ANOVAs and tukeys tests on the data. My descriptive stats will run, but thats as far as it will go. 

Here is my code so far:

Data GLANDES_TRUIE;
	infile "/home/u62306126/sasuser.v94/LYS3/glande_stats.csv" dlm="," firstobs=2;
	input TRUIE TRAIT ADN_PAR_SEC ARN_PAR_SEC BW NBR_TET
      PCT_GRAS_SEC PCT_MS PCT_PROT_SEC PDS_EXTRA PDS_PAR PDS_PAR_TET  
      RATIO_ARN_ADN RATIO_EXTRA_PAR RATIO_PROT_ADN RATIO_PROT_ARN
      TOT_ADN_PAR TOT_ADN_TET TOT_ARN_PAR TOT_ARN_TET TOT_GRAS_PAR TOT_PROT_PAR;
Run;

PROC CONTENTS; run;
data GLANDES_TRUIE;
  set lecture_GLANDES;
  if TRAIT=1 then TRT="CONTROL";
  if TRAIT=2 then TRT="SOYBEAN";
  if TRAIT=3 then TRT="CASEIN";
  if TRAIT=4 then TRT="LYSINE";
  trt_TRUIE=compress(SUBSTR(TRT,1,3)||"_"||truie);
proc print;
run;

/* descriptive stats */
proc means data=GLANDES_TRUIE maxdec=2;
  class TRAIT;
  var ADN_PAR_SEC ARN_PAR_SEC BW NBR_TET
      PCT_GRAS_SEC PCT_MS PCT_PROT_SEC PDS_EXTRA PDS_PAR PDS_PAR_TET  
      RATIO_ARN_ADN RATIO_EXTRA_PAR RATIO_PROT_ADN RATIO_PROT_ARN
      TOT_ADN_PAR TOT_ADN_TET TOT_ARN_PAR TOT_ARN_TET TOT_GRAS_PAR TOT_PROT_PAR;
run;

/* descriptive stats separate tables for each variable */
proc sort data=GLANDES_TRUIE;
  by variable trait trt truie;
run;

proc means data=GLANDES_TRUIE maxdec=2;
  class trt;
  var GLANDE;
  BY variable;
run;

/* each variable analyzed separately */
proc sort data=GLANDES_TRUIE;
  BY variable;
proc mixed data=GLANDES_TRUIE;
  class TRAIT truie;
  model GLANDE=TRAIT/ outp=outpred;
  repeated / group=TRAIT;
  ods output tests3=tests;
  lsmeans TRAIT / cl;
  ods output lsmeans=lsm;
  BY variable;
run;

/* non-parametric analysis */
proc npar1way DATA=GLANDES_TRUIE wilcoxon;
  class TRT;
  var GLANDE;                                                                                                     
  by variable;     
ods output WilcoxonTest=WilcoxonTest (rename=nValue1=Wilcoxon);
run;

proc print data=WilcoxonTest noobs; 
  where name1="PT2_WIL";
  var variable;
  var Wilcoxon /  style(Column)=[background=colorFMT.];
  format Wilcoxon 6.4; 
run;

Thank you!!

Caroline 

[Quentin]

Hi, when you say "that's as far as it will go", what happens after that?  If you look at the log, do you see ERROR messages?  One of the most important parts of learning SAS learning how to read the log.  You always want to review your log before you look at any results.  If you the log has ERRORs or WARNINGs, you need to fix them, before you trust your results.

If you look at your log and can't figure out what it means, please paste the log into a post here, and people can help you.  One thing I noticed if you have a lot of code like:

proc sort data=GLANDES_TRUIE;
  by variable trait trt truie;    * <-- you do not have a variable named VARIABLE ;
run;

The second line is a BY statement, commonly used in SAS for processing data in groups, or in this case for sorting data into groups.  A BY statement expects the list of words after the word BY to be the names of variables that exist in the input data.  With this code, it will expect the data to have a variable named VARIABLE.  I don't think that exists in your data, which should trigger an error message.  Perhaps try:

proc sort data=GLANDES_TRUIE;
  by trait trt truie;  * <-- removed the word VARIABLE ;
run;

proc means data=GLANDES_TRUIE maxdec=2;
  class trt;
  var GLANDE;
  BY trait trt truie;  * <-- replaced the word VARIABLE with the list of variables you sorted by above;
run;

Note also above that the CLASS statement and BY statement have similar purposes in PROC MEANS.  While they could be used together, it's unlikely this will give you the result you want.  It would probably be better for you too think about the groups you want to have PROC MEANS output for, and then use either a CLASS statement or BY statement to define those groups.

[PaigeMiller]

Please be specific and tell us what EXACT part of your code doesn't work. Also please tell us what about this doesn't work — are there errors in the log? do you get output but its the wrong output?

If you get errors in the log, please show us the ENTIRE log for this PROC, copy the log as text and paste it into the window that appears when you click on the </> icon.

If the code produces output but its the wrong output, show us the output and explain what you think is wrong.

[caroline_rg]

@PaigeMiller @Quentin -- thank you for taking the time to look at this

Here is my output from the log when I try to run my data:

 
 1          OPTIONS NONOTES NOSTIMER NOSOURCE NOSYNTAXCHECK;
 NOTE: ODS statements in the SAS Studio environment may disable some output features.
 69         
 70         Data GLANDES_TRUIE;
 71         infile "/home/u62306126/sasuser.v94/LYS3/glande_stats.csv" dlm="," firstobs=2;
 72         input TRUIE TRAIT ADN_PAR_SEC ARN_PAR_SEC BW NBR_TET
 73               PCT_GRAS_SEC PCT_MS PCT_PROT_SEC PDS_EXTRA PDS_PAR PDS_PAR_TET
 74               RATIO_ARN_ADN RATIO_EXTRA_PAR RATIO_PROT_ADN RATIO_PROT_ARN
 75               TOT_ADN_PAR TOT_ADN_TET TOT_ARN_PAR TOT_ARN_TET TOT_GRAS_PAR TOT_PROT_PAR;
 76         Run;
 
 NOTE: The infile "/home/u62306126/sasuser.v94/LYS3/glande_stats.csv" is:
       Filename=/home/u62306126/sasuser.v94/LYS3/glande_stats.csv,
       Owner Name=u62306126,Group Name=oda,
       Access Permission=-rw-r--r--,
       Last Modified=09Feb2024:13:41:07,
       File Size (bytes)=8809
 
 NOTE: 64 records were read from the infile "/home/u62306126/sasuser.v94/LYS3/glande_stats.csv".
       The minimum record length was 52.
       The maximum record length was 136.
 NOTE: SAS went to a new line when INPUT statement reached past the end of a line.
 NOTE: The data set WORK.GLANDES_TRUIE has 63 observations and 22 variables.
 NOTE: DATA statement used (Total process time):
       real time           0.00 seconds
       user cpu time       0.00 seconds
       system cpu time     0.00 seconds
       memory              764.62k
       OS Memory           21668.00k
       Timestamp           02/11/2024 05:00:50 PM
       Step Count                        41  Switch Count  2
       Page Faults                       0
       Page Reclaims                     122
       Page Swaps                        0
       Voluntary Context Switches        15
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           264
       
 
 77         
 78         PROC CONTENTS; run;
 
 NOTE: PROCEDURE CONTENTS used (Total process time):
       real time           0.02 seconds
       user cpu time       0.03 seconds
       system cpu time     0.00 seconds
       memory              1743.93k
       OS Memory           21928.00k
       Timestamp           02/11/2024 05:00:50 PM
       Step Count                        42  Switch Count  0
       Page Faults                       0
       Page Reclaims                     125
       Page Swaps                        0
       Voluntary Context Switches        0
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           16
       
 
 79         data GLANDES_TRUIE;
 80           set lecture_GLANDES;
 ERROR: File WORK.LECTURE_GLANDES.DATA does not exist.
 81           if TRAIT=1 then TRT="CONTROL";
 82           if TRAIT=2 then TRT="SOYBEAN";
 83           if TRAIT=3 then TRT="CASEIN";
 84           if TRAIT=4 then TRT="LYSINE";
 85           trt_TRUIE=compress(SUBSTR(TRT,1,3)||"_"||truie);
 
 NOTE: Numeric values have been converted to character values at the places given by: (Line):(Column).
       85:44   
 NOTE: The SAS System stopped processing this step because of errors.
 WARNING: The data set WORK.GLANDES_TRUIE may be incomplete.  When this step was stopped there were 0 observations and 4 variables.
 WARNING: Data set WORK.GLANDES_TRUIE was not replaced because this step was stopped.
 NOTE: DATA statement used (Total process time):
       real time           0.00 seconds
       user cpu time       0.00 seconds
       system cpu time     0.00 seconds
       memory              633.96k
       OS Memory           21668.00k
       Timestamp           02/11/2024 05:00:50 PM
       Step Count                        43  Switch Count  0
       Page Faults                       0
       Page Reclaims                     58
       Page Swaps                        0
       Voluntary Context Switches        0
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           16
       
 
 
 86         proc print;
 87         run;
 
 NOTE: There were 63 observations read from the data set WORK.GLANDES_TRUIE.
 NOTE: PROCEDURE PRINT used (Total process time):
       real time           0.11 seconds
       user cpu time       0.12 seconds
       system cpu time     0.00 seconds
       memory              815.25k
       OS Memory           21924.00k
       Timestamp           02/11/2024 05:00:50 PM
       Step Count                        44  Switch Count  0
       Page Faults                       0
       Page Reclaims                     96
       Page Swaps                        0
       Voluntary Context Switches        0
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           96
       
 
 88         
 89         /* simpler code from stats lectures */
 90         Proc glimmix data=GLANDES_TRUIE;
 91         class TRAIT TRUIE;
 92         model ADN_PAR_SEC ARN_PAR_SEC BW NBR_TET
                              ___________
                              73
 NOTE: PROCEDURE GLIMMIX used (Total process time):
       real time           0.00 seconds
       user cpu time       0.00 seconds
       system cpu time     0.00 seconds
       memory              649.84k
       OS Memory           21924.00k
       Timestamp           02/11/2024 05:00:50 PM
       Step Count                        45  Switch Count  0
       Page Faults                       0
       Page Reclaims                     134
       Page Swaps                        0
       Voluntary Context Switches        0
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           0
       
 NOTE: The SAS System stopped processing this step because of errors.
 ERROR 73-322: Expecting an =.
 93               PCT_GRAS_SEC PCT_MS PCT_PROT_SEC PDS_EXTRA PDS_PAR PDS_PAR_TET
 94               RATIO_ARN_ADN RATIO_EXTRA_PAR RATIO_PROT_ADN RATIO_PROT_ARN
 95               TOT_ADN_PAR TOT_ADN_TET TOT_ARN_PAR TOT_ARN_TET TOT_GRAS_PAR TOT_PROT_PAR=TRAIT;
                                                                                           _
                                                                                           22
                                                                                           200
 ERROR 22-322: Syntax error, expecting one of the following: a name, ;, (, *, -, /, :, @, _CHARACTER_, _CHAR_, _NUMERIC_, |.  
 ERROR 200-322: The symbol is not recognized and will be ignored.
 96         covtest "block=0" 0.;
 97         lsmeans TRUIE/pdiff adjust=tukey lines;
 98         Run;
 99         
 100        /* descriptive stats */
 
 
 101        proc means data=GLANDES_TRUIE maxdec=2;
 102          class TRAIT;
 103          var ADN_PAR_SEC ARN_PAR_SEC BW NBR_TET
 104              PCT_GRAS_SEC PCT_MS PCT_PROT_SEC PDS_EXTRA PDS_PAR PDS_PAR_TET
 105              RATIO_ARN_ADN RATIO_EXTRA_PAR RATIO_PROT_ADN RATIO_PROT_ARN
 106              TOT_ADN_PAR TOT_ADN_TET TOT_ARN_PAR TOT_ARN_TET TOT_GRAS_PAR TOT_PROT_PAR;
 107        run;
 
 NOTE: There were 63 observations read from the data set WORK.GLANDES_TRUIE.
 NOTE: PROCEDURE MEANS used (Total process time):
       real time           0.09 seconds
       user cpu time       0.09 seconds
       system cpu time     0.00 seconds
       memory              6715.43k
       OS Memory           27568.00k
       Timestamp           02/11/2024 05:00:51 PM
       Step Count                        46  Switch Count  1
       Page Faults                       0
       Page Reclaims                     1579
       Page Swaps                        0
       Voluntary Context Switches        34
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           32
       
 
 108        
 109        /* descriptive stats separate tables for each variable */
 110        proc sort data=GLANDEs_truie;
 111          by trait truie;
 112        run;
 
 NOTE: There were 63 observations read from the data set WORK.GLANDES_TRUIE.
 NOTE: The data set WORK.GLANDES_TRUIE has 63 observations and 22 variables.
 NOTE: PROCEDURE SORT used (Total process time):
       real time           0.00 seconds
       user cpu time       0.00 seconds
       system cpu time     0.00 seconds
       memory              933.78k
       OS Memory           22696.00k
       Timestamp           02/11/2024 05:00:51 PM
       Step Count                        47  Switch Count  2
       Page Faults                       0
       Page Reclaims                     113
       Page Swaps                        0
       Voluntary Context Switches        12
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           264
       
 
 113        
 114        proc means data=GLANDES_TRUIE maxdec=2;
 115          class TRAIT;
 116          var GLANDE;
 ERROR: Variable GLANDE not found.
 117          BY TRAIT TRUIE;
 118        run;
 
 NOTE: The SAS System stopped processing this step because of errors.
 NOTE: PROCEDURE MEANS used (Total process time):
       real time           0.00 seconds
       user cpu time       0.00 seconds
       system cpu time     0.00 seconds
       memory              500.34k
       OS Memory           22436.00k
       Timestamp           02/11/2024 05:00:51 PM
       Step Count                        48  Switch Count  0
       Page Faults                       0
       Page Reclaims                     50
       Page Swaps                        0
       Voluntary Context Switches        0
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           0
       
 119        
 120        /* each variable analyzed separately */
 
 
 121        proc sort data=GLANDES_TRUIE;
 122          BY variable;
 ERROR: Variable VARIABLE not found.
 
 NOTE: The SAS System stopped processing this step because of errors.
 NOTE: PROCEDURE SORT used (Total process time):
       real time           0.00 seconds
       user cpu time       0.01 seconds
       system cpu time     0.00 seconds
       memory              437.50k
       OS Memory           22436.00k
       Timestamp           02/11/2024 05:00:51 PM
       Step Count                        49  Switch Count  0
       Page Faults                       0
       Page Reclaims                     49
       Page Swaps                        0
       Voluntary Context Switches        0
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           0
       
 
 
 123        proc mixed data=GLANDES_TRUIE;
 124          class TRAIT truie;
 125          model GLANDE=TRAIT/ outp=outpred;
 ERROR: Variable GLANDE not found.
 NOTE: PROCEDURE MIXED used (Total process time):
       real time           0.00 seconds
       user cpu time       0.00 seconds
       system cpu time     0.00 seconds
       memory              487.12k
       OS Memory           22436.00k
       Timestamp           02/11/2024 05:00:51 PM
       Step Count                        50  Switch Count  0
       Page Faults                       0
       Page Reclaims                     49
       Page Swaps                        0
       Voluntary Context Switches        0
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           8
       
 NOTE: The SAS System stopped processing this step because of errors.
 WARNING: The data set WORK.OUTPRED may be incomplete.  When this step was stopped there were 0 observations and 0 variables.
 WARNING: Data set WORK.OUTPRED was not replaced because this step was stopped.
 126          repeated / group=TRAIT;
 127          ods output tests3=tests;
 128          lsmeans TRAIT / cl;
 129          ods output lsmeans=lsm;
 130          BY variable;
 131        run;
 132        
 133        /* non-parametric analysis */
 
 
 134        proc npar1way DATA=GLANDES_TRUIE wilcoxon;
 135          class TRAIT;
 136          var GLANDE;
 ERROR: Variable GLANDE not found.
 137          by TRAIT TRUIE;
 138        ods output WilcoxonTest=WilcoxonTest (rename=nValue1=Wilcoxon);
 139        run;
 
 NOTE: The SAS System stopped processing this step because of errors.
 NOTE: PROCEDURE NPAR1WAY used (Total process time):
       real time           0.00 seconds
       user cpu time       0.00 seconds
       system cpu time     0.00 seconds
       memory              442.40k
       OS Memory           22436.00k
       Timestamp           02/11/2024 05:00:51 PM
       Step Count                        51  Switch Count  1
       Page Faults                       0
       Page Reclaims                     48
       Page Swaps                        0
       Voluntary Context Switches        7
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           0
       
 WARNING: Output 'WilcoxonTest' was not created.  Make sure that the output object name, label, or path is spelled correctly.  Also, 
          verify that the appropriate procedure options are used to produce the requested output object.  For example, verify that 
          the NOPRINT option is not used.
 WARNING: Output 'lsmeans' was not created.  Make sure that the output object name, label, or path is spelled correctly.  Also, 
          verify that the appropriate procedure options are used to produce the requested output object.  For example, verify that 
          the NOPRINT option is not used.
 WARNING: Output 'tests3' was not created.  Make sure that the output object name, label, or path is spelled correctly.  Also, 
          verify that the appropriate procedure options are used to produce the requested output object.  For example, verify that 
          the NOPRINT option is not used.
 140        
 
 
 141        proc print data=WilcoxonTest noobs;
 ERROR: File WORK.WILCOXONTEST.DATA does not exist.
 142          where name1="PT2_WIL";
 WARNING: No data sets qualify for WHERE processing.
 143          var TRAIT TRUIE;
 144          var Wilcoxon /  style(Column)=[background=colorFMT.];
                                             __________
                                             22
                                             202
 ERROR 22-322: Syntax error, expecting one of the following: ;, STYLE.  
 ERROR 202-322: The option or parameter is not recognized and will be ignored.
 145          format Wilcoxon 6.4;
 146        run;
 
 NOTE: The SAS System stopped processing this step because of errors.
 NOTE: PROCEDURE PRINT used (Total process time):
       real time           0.00 seconds
       user cpu time       0.00 seconds
       system cpu time     0.00 seconds
       memory              228.84k
       OS Memory           22176.00k
       Timestamp           02/11/2024 05:00:51 PM
       Step Count                        52  Switch Count  0
       Page Faults                       0
       Page Reclaims                     16
       Page Swaps                        0
       Voluntary Context Switches        0
       Involuntary Context Switches      0
       Block Input Operations            0
       Block Output Operations           8
       
 147        
 148        OPTIONS NONOTES NOSTIMER NOSOURCE NOSYNTAXCHECK;
 158        

[PaigeMiller]

 79         data GLANDES_TRUIE;
 80           set lecture_GLANDES;
 ERROR: File WORK.LECTURE_GLANDES.DATA does not exist.

The data set lecture_glandes does not exist. You have to fix this in order for the rest of your code to work properly.

[Quentin]

Another lesson in SAS is that you rarely (never) want to write an entire program and run it all.  Because a problem in step #2 will make everything after it useless.  It's much easier to write the first DATA step, run it, and debug it.  Then write the next step, run it, and debug it.  After you have all the steps working, it's a good idea to start a new SAS session and run them all at once.  But while you're writing code, running each step one-at-a-time as you are writing is usually more helpful than running the whole program.

[caroline_rg]

Thank you! I've fixed that. The error message:

ERROR 73-322: Expecting an =.
 73               PCT_GRAS_SEC PCT_MS PCT_PROT_SEC PDS_EXTRA PDS_PAR PDS_PAR_TET
 74               RATIO_ARN_ADN RATIO_EXTRA_PAR RATIO_PROT_ADN RATIO_PROT_ARN
 75               TOT_ADN_PAR TOT_ADN_TET TOT_ARN_PAR TOT_ARN_TET TOT_GRAS_PAR TOT_PROT_PAR=TRAIT/outp=outpred;

Is relating to this section of code:

ERROR 73-322: Expecting an =.
 73               PCT_GRAS_SEC PCT_MS PCT_PROT_SEC PDS_EXTRA PDS_PAR PDS_PAR_TET
 74               RATIO_ARN_ADN RATIO_EXTRA_PAR RATIO_PROT_ADN RATIO_PROT_ARN
 75               TOT_ADN_PAR TOT_ADN_TET TOT_ARN_PAR TOT_ARN_TET TOT_GRAS_PAR TOT_PROT_PAR=TRAIT/outp=outpred;

I am confused as to why it says it is expecting a "=". There is an equal sign between the variables and trait 

[yabwon]

According to GLIMMIX documentation: https://documentation.sas.com/doc/en/statcdc/14.2/statug/statug_glimmix_syntax15.htm

the syntax is:

MODEL response <(response-options)> = <fixed-effects> </ model-options>;

e.g.,

model y=x / ALPHA=0.07;

And, if I see it correctly in your log, you don't have it in this form.

Bart

[caroline_rg]

Hi Bart,
Are you able to explain how it is not in this form? All of my variables (the "y") are equal to the trait (the "x"). I have changed the code to have "/alpha=0.05", but get the same error message. I'm not sure why SAS isn't recognizing my "=" between the y and x

[Tom]

---

@caroline_rg wrote:
Hi Bart,
Are you able to explain how it is not in this form? All of my variables (the "y") are equal to the trait (the "x"). I have changed the code to have "/alpha=0.05", but get the same error message. I'm not sure why SAS isn't recognizing my "=" between the y and x

---

Because you don't have one.

 92         model ADN_PAR_SEC ARN_PAR_SEC BW NBR_TET
 93               PCT_GRAS_SEC PCT_MS PCT_PROT_SEC PDS_EXTRA PDS_PAR PDS_PAR_TET
 94               RATIO_ARN_ADN RATIO_EXTRA_PAR RATIO_PROT_ADN RATIO_PROT_ARN
 95               TOT_ADN_PAR TOT_ADN_TET TOT_ARN_PAR TOT_ARN_TET TOT_GRAS_PAR TOT_PROT_PAR=TRAIT;
 

Which of those variables is the DEPENDENT variable (the one that the model is going to predict the value for)?  Place that before the = and then list the INEDEPENDENT variables (the ones used as the basis for the predictions) after the =.

[PaigeMiller]

---

@caroline_rg wrote:
Hi Bart,
Are you able to explain how it is not in this form? All of my variables (the "y") are equal to the trait (the "x"). I have changed the code to have "/alpha=0.05", but get the same error message. I'm not sure why SAS isn't recognizing my "=" between the y and x

---

In PROC GLIMMIX (as shown by @yabwon by quoting the SAS documentation), you can have only a single Y variable. You cannot have multiple Y variables. So, assuming the Y variable is ADN_PAR_SEC the command you want is

model ADN_PAR_SEC = BW NBR_TET ... ;

and then you include BW and NBR_TET and all the rest of the X-variables (also called independent variables) in the model statement.

NOTE: Your code actually began with

 model ADN_PAR_SEC ARN_PAR_SEC BW NBR_TET

and the first two variables are identical, and you cannot enter a variable into the model statement more than once.

[caroline_rg]

Thank you!