Interestingly, I am not having the problem now after coming back to my computer and restarting SAS to produce the log you wanted. I am just in the beginning of putting this code together and thus was revising and resubmitting code. The code I posted was not working and I still am not sure why. For what it might be worth, here is the log as requested but which is now working.
NOTE: Copyright (c) 2016 by SAS Institute Inc., Cary, NC, USA.
NOTE: SAS (r) Proprietary Software 9.4 (TS1M5)
NOTE: This session is executing on the X64_7PRO platform.
NOTE: Updated analytical products:
SAS/STAT 14.3
SAS/ETS 14.3
SAS/OR 14.3
SAS/IML 14.3
SAS/QC 14.3
NOTE: Additional host information:
X64_7PRO WIN 6.1.7601 Service Pack 1 Workstation
NOTE: SAS initialization used:
real time 1.30 seconds
cpu time 0.59 seconds
1 ods graphics / antialiasmax=500000 ;
2
3 footnote'TID6164';
4 footnote2'Protocol restarted after 21 hours due to power outage.';
5 footnote3'Data before 21 hours not included in this analysis';
6 **** 1a) Import, transpose and rename the raw data ;
7 PROC IMPORT OUT= WORK.RAWWide
8 DATAFILE= "J:\SchneiderLab\Edith Orozco\QuIC assay\RT-QuIC m
9 erged runs in excel\TID6164.xlsx"
10 DBMS=EXCELCS REPLACE;
11 RANGE='SAS$B3:CT119'n;
12 SCANTEXT=YES;
13 USEDATE=YES;
14 SCANTIME=YES;
15 RUN;
NOTE: WORK.RAWWIDE data set was successfully created.
NOTE: The data set WORK.RAWWIDE has 116 observations and 97 variables.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.76 seconds
cpu time 0.09 seconds
16
17 data RAWWide;
18 set RAWWide ;
19 attrib time format=time8. informat=8. ;
20 time = (Time__h_ * '01:00:00't) + '21:00:00't ; /* Convert decimal minutes to SAS time
20 ! */
21 drop Time__h_ ;
22 run;
NOTE: There were 116 observations read from the data set WORK.RAWWIDE.
NOTE: The data set WORK.RAWWIDE has 116 observations and 97 variables.
NOTE: DATA statement used (Total process time):
real time 0.06 seconds
cpu time 0.01 seconds
23 proc sort data=RAWWide ;
24 by time ;
25 run;
NOTE: There were 116 observations read from the data set WORK.RAWWIDE.
NOTE: The data set WORK.RAWWIDE has 116 observations and 97 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.04 seconds
cpu time 0.03 seconds
26 proc transpose data=RAWWide out=RAWLong;
27 var Sample_X1-Sample_X96 ;
28 by time ;
29 run;
NOTE: There were 116 observations read from the data set WORK.RAWWIDE.
NOTE: The data set WORK.RAWLONG has 11136 observations and 4 variables.
NOTE: PROCEDURE TRANSPOSE used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds
30 data RAWLong ;
31 set RAWLong (rename=(COL1=RFU));
32 attrib sample_ID format=8. label='sample_ID X##';
33 Sample_ID=substr(_NAME_,9);
34 drop _LABEL_ _NAME_ ;
35 run;
NOTE: Character values have been converted to numeric values at the places given by:
(Line):(Column).
33:15
NOTE: There were 11136 observations read from the data set WORK.RAWLONG.
NOTE: The data set WORK.RAWLONG has 11136 observations and 3 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds
36
37 **** 1b) Import, transpose and rename the layout data ;
38 PROC IMPORT OUT= WORK.Layout
39 DATAFILE= "J:\SchneiderLab\Edith Orozco\QuIC assay\RT-QuIC m
40 erged runs in excel\TID6164.xlsx"
41 DBMS=EXCELCS REPLACE;
42 RANGE="Layout$";
43 SCANTEXT=YES;
44 USEDATE=YES;
45 SCANTIME=YES;
46 RUN;
NOTE: WORK.LAYOUT data set was successfully created.
NOTE: The data set WORK.LAYOUT has 96 observations and 11 variables.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.56 seconds
cpu time 0.06 seconds
47
48 **** 1c) Put 1a and 1b together;
49 proc sort data=RAWLong ; by sample_ID time ; run;
NOTE: There were 11136 observations read from the data set WORK.RAWLONG.
NOTE: The data set WORK.RAWLONG has 11136 observations and 3 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.06 seconds
cpu time 0.01 seconds
50 proc sort data=Layout ; by sample_ID ; run;
NOTE: There were 96 observations read from the data set WORK.LAYOUT.
NOTE: The data set WORK.LAYOUT has 96 observations and 11 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.04 seconds
cpu time 0.00 seconds
51 data rfu ;
52 merge Layout RAWLong ;
53 by sample_ID ;
54 attrib dilution format=E7. ;
55 run;
NOTE: There were 96 observations read from the data set WORK.LAYOUT.
NOTE: There were 11136 observations read from the data set WORK.RAWLONG.
NOTE: The data set WORK.RFU has 11136 observations and 13 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds
56
57 proc sort data=rfu ;
58 by status dilution replicate time ;
59 run;
NOTE: There were 11136 observations read from the data set WORK.RFU.
NOTE: The data set WORK.RFU has 11136 observations and 13 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.03 seconds
cpu time 0.01 seconds
60 proc freq data=rfu ;
61 by status dilution ;
62 table replicate / nopercent nocol norow nocum ;
63 run;
NOTE: Writing HTML Body file: sashtml.htm
NOTE: There were 11136 observations read from the data set WORK.RFU.
NOTE: PROCEDURE FREQ used (Total process time):
real time 0.56 seconds
cpu time 0.10 seconds
64 proc sgpanel data=rfu ;
65 title'PLOT 1: Raw data (n=12 or 16 t reps)';
66 by status;
67 panelby dilution / novarname columns=1 uniscale=all;
68 series x=time y=rfu / group=replicate ;
69 colaxis type=time tickvalueformat=time8. grid display=(novalues) ;
70 rowaxis values=(0 to 260000 by 25000) grid display=(novalues) ;
71 run;
NOTE: PROCEDURE SGPANEL used (Total process time):
real time 3.28 seconds
cpu time 0.28 seconds
NOTE: There were 11136 observations read from the data set WORK.RFU.
72 title;
73 proc freq data=rfu ;
74 table sample_id / nocum norow nocol nopercent ;
75 table row*well / nocum norow nocol nopercent ;
76 run;
ERROR: Permanent copy of file WORK.'SASTMP-000000018'n.UTILITY was deleted.
ERROR: Permanent copy of file WORK.'SASTMP-000000018'n.UTILITY was deleted.
NOTE: The SAS System stopped processing this step because of errors.
NOTE: PROCEDURE FREQ used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds
77 /*/*/*/*/* 1d) check for time line glitch */*/*/*/*/;
78 data lag ;
79 set rfu ;
80 attrib lagdif format=time8. informat=8.;
81 lagdif = time - lag(time) ;
82 if time='21:00:00't then lagdif=. ;
83 run;
NOTE: Missing values were generated as a result of performing an operation on missing values.
Each place is given by: (Number of times) at (Line):(Column).
1 at 81:19
NOTE: There were 11136 observations read from the data set WORK.RFU.
NOTE: The data set WORK.LAG has 11136 observations and 14 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds
84 proc sort data=lag ;
85 by sample_ID time ;
86 run;
NOTE: There were 11136 observations read from the data set WORK.LAG.
NOTE: The data set WORK.LAG has 11136 observations and 14 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.18 seconds
cpu time 0.03 seconds
87 proc sgplot data=lag ;
88 series x=time y=lagdif / group=sample_id ;
89 yaxis values=('00:00:00't to '01:30:00't by '00:10:00't);
90 run;
NOTE: PROCEDURE SGPLOT used (Total process time):
real time 1.10 seconds
cpu time 0.06 seconds
NOTE: The column format TIME8 is replaced by an auto-generated format on the axis.
NOTE: Some graph legends have been dropped due to size constraints. Try adjusting the
MAXLEGENDAREA=, WIDTH= and HEIGHT= options in the ODS GRAPHICS statement.
NOTE: There were 11136 observations read from the data set WORK.LAG.
91
92 /*/*/*/*/* 1e) fix time line glitch */*/*/*/*/;
93 data rfu1 ;
94 set lag ;
95 by sample_ID;
96 attrib lag_time format=time8. informat=8. ;
97 lag_time=lag(time);
98 if lagdif>'00:45:00't then time=(lag_time+'00:43:12't) ;
99 else time=time;
100 drop lagdif lag_time ;
101 run;
NOTE: There were 11136 observations read from the data set WORK.LAG.
NOTE: The data set WORK.RFU1 has 11136 observations and 13 variables.
NOTE: DATA statement used (Total process time):
real time 0.03 seconds
cpu time 0.01 seconds
102 proc sort data=rfu1 ;
103 by sample_ID time ;
104 run;
NOTE: There were 11136 observations read from the data set WORK.RFU1.
NOTE: The data set WORK.RFU1 has 11136 observations and 13 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds
105 data lag1 ;
106 set rfu1 ;
107 attrib lagdif format=time8. informat=8.;
108 lagdif = time - lag(time) ;
109 if time='00:00:00't then lagdif=. ;
110 run;
NOTE: Missing values were generated as a result of performing an operation on missing values.
Each place is given by: (Number of times) at (Line):(Column).
1 at 108:19
NOTE: There were 11136 observations read from the data set WORK.RFU1.
NOTE: The data set WORK.LAG1 has 11136 observations and 14 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds
111 proc sort data=lag1 ;
112 by sample_ID time ;
113 run;
NOTE: There were 11136 observations read from the data set WORK.LAG1.
NOTE: The data set WORK.LAG1 has 11136 observations and 14 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds
114 proc sgplot data=lag1 ;
115 series x=time y=lagdif / group=sample_id ;
116 yaxis values=('00:00:00't to '01:30:00't by '00:10:00't);
117 run;
NOTE: PROCEDURE SGPLOT used (Total process time):
real time 0.88 seconds
cpu time 0.04 seconds
NOTE: The column format TIME8 is replaced by an auto-generated format on the axis.
NOTE: Some graph legends have been dropped due to size constraints. Try adjusting the
MAXLEGENDAREA=, WIDTH= and HEIGHT= options in the ODS GRAPHICS statement.
NOTE: There were 11136 observations read from the data set WORK.LAG1.
118
119 data rfu2 ;
120 set lag1 ;
121 by sample_ID;
122 attrib lag_time format=time8. informat=8. ;
123 lag_time=lag(time);
124 if lagdif>'00:45:00't then time=(lag_time+'00:43:12't) ;
125 else time=time;
126 drop lagdif lag_time ;
127 run;
NOTE: There were 11136 observations read from the data set WORK.LAG1.
NOTE: The data set WORK.RFU2 has 11136 observations and 13 variables.
NOTE: DATA statement used (Total process time):
real time 0.03 seconds
cpu time 0.03 seconds
128 proc sort data=rfu2 ;
129 by sample_ID time ;
130 run;
NOTE: There were 11136 observations read from the data set WORK.RFU2.
NOTE: The data set WORK.RFU2 has 11136 observations and 13 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds
131 data lag2 ;
132 set rfu2 ;
133 attrib lagdif format=time8. informat=8.;
134 lagdif = time - lag(time) ;
135 if time='00:00:00't then lagdif=. ;
136 run;
NOTE: Missing values were generated as a result of performing an operation on missing values.
Each place is given by: (Number of times) at (Line):(Column).
1 at 134:19
NOTE: There were 11136 observations read from the data set WORK.RFU2.
NOTE: The data set WORK.LAG2 has 11136 observations and 14 variables.
NOTE: DATA statement used (Total process time):
real time 0.04 seconds
cpu time 0.00 seconds
137 proc sort data=lag2 ;
138 by sample_ID time ;
139 run;
NOTE: There were 11136 observations read from the data set WORK.LAG2.
NOTE: The data set WORK.LAG2 has 11136 observations and 14 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.04 seconds
cpu time 0.01 seconds
140 proc sgplot data=lag2 ;
141 series x=time y=lagdif / group=sample_id ;
142 yaxis values=('00:00:00't to '01:30:00't by '00:10:00't);
143 run;
NOTE: PROCEDURE SGPLOT used (Total process time):
real time 0.92 seconds
cpu time 0.06 seconds
NOTE: The column format TIME8 is replaced by an auto-generated format on the axis.
NOTE: Some graph legends have been dropped due to size constraints. Try adjusting the
MAXLEGENDAREA=, WIDTH= and HEIGHT= options in the ODS GRAPHICS statement.
NOTE: There were 11136 observations read from the data set WORK.LAG2.
144
145 proc freq data=rfu2 ;
146 table sample_id / nocum norow nocol nopercent ;
147 table row*well / nocum norow nocol nopercent ;
148 run;
NOTE: There were 11136 observations read from the data set WORK.RFU2.
NOTE: PROCEDURE FREQ used (Total process time):
real time 0.31 seconds
cpu time 0.04 seconds
149
150 **** 2) Visually determine time frame of baseline after rapid ThT decay and before earliest
150! rxn;
151 proc sort data=rfu2 ;
152 by status row well time ;
153 run;
NOTE: There were 11136 observations read from the data set WORK.RFU2.
NOTE: The data set WORK.RFU2 has 11136 observations and 13 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.04 seconds
cpu time 0.01 seconds
154 proc sgplot data=rfu2 noautolegend ;
155 title'PLOT 2a: Visually determined maximum RFU for NEG vs POS';
156 by status;
157 refline 26000 / axis=y label="Max NEG-RFU reading";
158 series x=time y=rfu / group=sample_ID ;
159 xaxis min='00:00:00't ;
160 run;
NOTE: PROCEDURE SGPLOT used (Total process time):
real time 1.70 seconds
cpu time 0.15 seconds
NOTE: The column format TIME8 is replaced by an auto-generated format on the axis.
NOTE: The column format TIME8 is replaced by an auto-generated format on the axis.
NOTE: The column format TIME8 is replaced by an auto-generated format on the axis.
NOTE: There were 11136 observations read from the data set WORK.RFU2.
161 title;title2;
162
163 proc sort data=rfu2 ;
164 by status dilution replicate ;
165 run;
NOTE: There were 11136 observations read from the data set WORK.RFU2.
NOTE: The data set WORK.RFU2 has 11136 observations and 13 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.06 seconds
cpu time 0.01 seconds
166 proc univariate data=rfu2 noprint ;
167 by status dilution replicate ;
168 var rfu ;
169 output out=max_RFU max=maxRFU ;
170 run;
NOTE: The data set WORK.MAX_RFU has 96 observations and 4 variables.
NOTE: PROCEDURE UNIVARIATE used (Total process time):
real time 0.03 seconds
cpu time 0.00 seconds
171
172 data max_RFU ;
173 set max_RFU ;
174 attrib misfolding_activity format=8. informat=8. label='misfolding activity';
175 if maxRFU>26000 then misfolding_activity = 1 ;
176 else misfolding_activity = 0;
177 run;
NOTE: There were 96 observations read from the data set WORK.MAX_RFU.
NOTE: The data set WORK.MAX_RFU has 96 observations and 5 variables.
NOTE: DATA statement used (Total process time):
real time 0.03 seconds
cpu time 0.03 seconds
178 proc sort data=max_RFU ;
179 by status dilution ;
180 run;
NOTE: There were 96 observations read from the data set WORK.MAX_RFU.
NOTE: The data set WORK.MAX_RFU has 96 observations and 5 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds
181 proc freq data=max_RFU ;
182 by status dilution ;
183 tables misfolding_activity / bin(level=1 cl=exact);
184 output out=freq bin ;
185 run;
NOTE: There were 96 observations read from the data set WORK.MAX_RFU.
NOTE: The data set WORK.FREQ has 7 observations and 12 variables.
NOTE: PROCEDURE FREQ used (Total process time):
real time 0.34 seconds
cpu time 0.06 seconds
186 quit;
187
188 proc genmod data=max_rfu ;
189 class status ;
190 model misfolding_activity = status dilution / dist=poisson ;
191 run;
NOTE: Algorithm converged.
NOTE: The scale parameter was held fixed.
NOTE: PROCEDURE GENMOD used (Total process time):
real time 0.45 seconds
cpu time 0.01 seconds
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