*** MARO SECTION ***

*MACRO1

DEFINE MACRO1 (!POS !CHAREND ('/'))
  !DO !I !IN (!1)

COMPUTE !I = LG10(!I).

!DOEND
!ENDDEFINE.

*MACRO2

DEFINE MACRO2 (!POS !CHAREND ('/'))
  
  !DO !I !IN (!1)  

GET
    FILE='C:\Applied Biosystems\SDS Documents\temp0.SAV'.

* NonLinear Regression.
MODEL PROGRAM Fmax=0.4 Chalv=29 K=2.0 Fb=-0.1 .
COMPUTE PRED_ = Fb + Fmax / (1 +2.71828 ** (-(CYCLE -  Chalv ) / K) ).
NLR !I
  /OUTFILE='C:\Applied Biosystems\SDS Documents\temp1.SAV'
  /PRED PRED_
  /CRITERIA SSCONVERGENCE 1E-8 PCON 1E-8 .
EXECUTE.

GET
  FILE='C:\Applied Biosystems\SDS Documents\temp1.SAV'.

ADD FILES FILE=* 
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP1.SAV'
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP1.SAV'
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP1.SAV'
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP1.SAV'.
EXECUTE.

DELETE VARIABLES Fmax Fb SSE NCASES.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP6.SAV'.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP7.SAV'
  /COMPRESSED.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP6.SAV'
  /COMPRESSED.

ADD FILES FILE=*
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP7.SAV'
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP7.SAV'.
EXECUTE.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP7.SAV'
  /COMPRESSED.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP6.SAV'
  /COMPRESSED.

ADD FILES FILE=*
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP7.SAV'
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP7.SAV'.
EXECUTE.

MATCH FILES FILE=* /FILE= 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\CYCLE.SAV' .
EXECUTE.

COMPUTE weight =  0.1+1/(1+2.7182818**(-(CYCLE-Chalv+6)/1.2)) + 10/(1+2.7182818**(-(Chalv-43)/1.2)).
EXECUTE .

DELETE VARIABLES Chalv K CASE_LBL .

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP2.sav'
  /COMPRESSED.

MATCH FILES FILE='C:\Applied Biosystems\SDS Documents\TEMP0.SAV' /FILE='C:\Applied Biosystems\SDS Documents\TEMP2.SAV'.
EXECUTE.

MISSING VALUES   A1 TO  H12   (0.0000000)  .

WEIGHT
  BY weight .

* NonLinear Regression.
MODEL PROGRAM Fmax=0.4 Chalv=29 K=2.0 Fb=-0.1 Base=0 .
COMPUTE PRED_ = Fb + CYCLE * Base + Fmax / (1 +2.7182818 ** (-(CYCLE -  Chalv ) / K) ).
NLR !I
  /OUTFILE='C:\Applied Biosystems\SDS Documents\temp1.SAV'
  /PRED PRED_
  /SAVE PRED_
  /CRITERIA SSCONVERGENCE 1E-8 PCON 1E-8 .
GRAPH
  /SCATTERPLOT(OVERLAY)=CYCLE CYCLE  WITH !I PRED_ (PAIR)
  /MISSING=LISTWISE .
EXECUTE.

ADD FILES FILE='C:\Applied Biosystems\SDS Documents\A_H.sav'
  /FILE='C:\Applied Biosystems\SDS Documents\temp1.sav'.
EXECUTE.
 
SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'
  /COMPRESSED.

!DOEND
!ENDDEFINE.

*MACRO3

DEFINE MACRO3 ( ).
!DO !I =1 !TO 5.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'
  /COMPRESSED.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP4.SAV'
  /COMPRESSED.

ADD FILES FILE=*
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'.
EXECUTE.

!DOEND.
!ENDDEFINE.

*** DATA IMPORT SECTION ***

GET DATA  /TYPE = TXT
 /FILE = 'C:\DATA\SDS EXPORT FILE.TXT'
 /DELCASE = LINE
 /DELIMITERS = "\t "
 /ARRANGEMENT = DELIMITED
 /FIRSTCASE = 3
 /IMPORTCASE = ALL
 /VARIABLES =  
   V1 F13.4
   V2 F13.4
   V3 F13.4
   V4 F13.4
   V5 F13.4
   V6 F13.4
   V7 F13.4
   V8 F13.4
   V9 F13.4
   V10 F13.4
   V11 F13.4
   V12 F13.4
   V13 F13.4
   V14 F13.4
   V15 F13.4
   V16 F13.4
   V17 F13.4
   V18 F13.4
   V19 F13.4
   V20 F13.4
   V21 F13.4
   V22 F13.4
   V23 F13.4
   V24 F13.4
   V25 F13.4
   V26 F13.4
   V27 F13.4
   V28 F13.4
   V29 F13.4
   V30 F13.4
   V31 F13.4
   V32 F13.4
   V33 F13.4
   V34 F13.4
   V35 F13.4
   V36 F13.4
   V37 F13.4
   V38 F13.4
   V39 F13.4
   V40 F13.4
   V41 F13.4
   V42 F13.4
   V43 F13.4
   V44 F13.4
   V45 F13.4
   V46 F13.4
   V47 F13.4
   V48 F13.4
 .
CACHE.
EXECUTE.

MATCH FILES FILE=* /FILE= 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\CASELBL.SAV' .
EXECUTE.

DELETE VARIABLES  V1 V2 V3.

FLIP
  VARIABLES= V4 TO V48  .

MATCH FILES FILE=* /FILE= 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\CYCLE.SAV' .
EXECUTE.

DELETE VARIABLES CASE_LBL . 

APPLY DICTIONARY FROM 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\DICT.SAV'.

*** LOG10 TRANSFORMATION ***

MACRO1 A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 A11 A12 B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 D1 D2 D3 D4 D5 D6 D7 D8 D9 D10 D11 D12 
  E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12 F1 F2 F3 F4 F5 F6 F7 F8 F9 F10 F11 F12 G1 G2 G3 G4 G5 G6 G7 G8 G9 G10 G11 G12 H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 H11 H12  /.
EXECUTE.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP0.sav'
 /COMPRESSED.

GET
    FILE='C:\Applied Biosystems\SDS Documents\A_H1.SAV'.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'.

*** CALCULATION OF CONVERSION FACTOR ***

MACRO2 A1 A2/.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP5.SAV'
  /COMPRESSED.

COMPUTE F0 = Fmax / (1 + 2.718281828 ** (Chalv / K)) .
EXECUTE .

COMPUTE CF = 100000 / F0 .
EXECUTE.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'
  /COMPRESSED.

GET
    FILE='C:\Applied Biosystems\SDS Documents\A_H1.SAV'.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'
  /COMPRESSED.

MACRO2 A3 A4 /.

ADD FILES FILE='C:\Applied Biosystems\SDS Documents\TEMP5.SAV'
  /FILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'.
EXECUTE.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP5.SAV'
  /COMPRESSED.

GET
    FILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'.

COMPUTE F0 = Fmax / (1 + 2.718281828 ** (Chalv / K)) .
EXECUTE .

COMPUTE CF = 1000 / F0 .
EXECUTE.

ADD FILES FILE=*
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'.
EXECUTE.

FLIP
  VARIABLES= CF.

MACRO1 VAR001 VAR002 VAR003 VAR004 /.

EXECUTE.

COMPUTE CFmean = MEAN(var001,var002,var003,var004) .
EXECUTE .

COMPUTE CFmean = 10**(CFmean).
EXECUTE.

DELETE VARIABLES CASE_LBL VAR001 VAR002 VAR003 VAR004 .

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'
  /COMPRESSED.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP4.SAV'
  /COMPRESSED.

ADD FILES FILE=*
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'.
EXECUTE.

MACRO3.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'
  /COMPRESSED.

Get
    FILE='C:\Applied Biosystems\SDS Documents\TEMP5.SAV'.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'.

*** NLR ON REMAINING REACTIONS ***

MACRO2 A5 A6 A7 A8 A9 A10 A11 A12 /.
MACRO2 B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12 /.
MACRO2 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 /.
MACRO2 D1 D2 D3 D4 D5 D6 D7 D8 D9 D10 D11 D12 /.
MACRO2 E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12 /.
MACRO2 F1 F2 F3 F4 F5 F6 F7 F8 F9 F10 F11 F12 /.
MACRO2 G1 G2 G3 G4 G5 G6 G7 G8 G9 G10 G11 G12 /.
MACRO2 H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 H11 H12 /.

*** CALCULATION OF COPY NUMBER ESTIMATES ***

MATCH FILES FILE=* /FILE='C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\TEMP3.SAV'.
EXECUTE .

APPLY DICTIONARY FROM = 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\16digits.SAV'.

COMPUTE F0 = Fmax / (1 + 2.718281828 ** (Chalv / K)) .
EXECUTE .

COMPUTE CONC = F0 * CFmean.
EXECUTE .

APPLY DICTIONARY FROM = 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\SAMPLE.SAV'.

MATCH FILES FILE=* /FILE='C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\CASELBL.SAV'.
EXECUTE .

DELETE VARIABLES  V1 NCASES.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\OUTPUT\A_H.SAV'.