*** MACRO 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=1.2 Chalv=30 K=2.0 Fb=0 . 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 = 0.24+0.76/(1+2.7182818**(-(CYCLE-Chalv+17)/4.5))-0.95/(1+2.7182818**(-(CYCLE-Chalv)/1.8))+2/(1+2.7182818**(-(Chalv-40)/3)). 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=1.2 Chalv=30 K=2.0 Fb=0 . COMPUTE PRED_ = Fb + 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 2X V2 3X V3 1X V4 10X V5 10X V6 10X V7 10X V8 10X V9 10X V10 10X V11 10X V12 10X V13 10X V14 10X V15 10X V16 10X V17 10X V18 10X V19 10X V20 10X V21 10X V22 10X V23 10X V24 10X V25 10X V26 10X V27 10X V28 10X V29 10X V30 10X V31 10X V32 10X V33 10X V34 10X V35 10X V36 10X V37 10X V38 10X V39 10X V40 10X V41 10X V42 10X V43 9X V44 10X V45 9X V46 10X V47 10X V48 10X V49 1X V50 F13.2 V51 F13.2 V52 F13.2 V53 F13.2 V54 F13.2 V55 F13.2 V56 F13.2 V57 F13.2 V58 F13.2 V59 F14.2 V60 F13.2 V61 F13.2 V62 F13.2 V63 F13.2 V64 F13.2 V65 F13.2 V66 F13.2 V67 F13.2 V68 F13.2 V69 F13.2 V70 F13.2 V71 F13.2 V72 F13.2 V73 F13.2 V74 F13.2 V75 F13.2 V76 F13.2 V77 F13.2 V78 F13.2 V79 F13.2 V80 F13.2 V81 F13.2 V82 F13.2 V83 F13.2 V84 F12.2 V85 F13.2 V86 F13.2 V87 F13.2 V88 F13.2 V89 F13.2 V90 F13.2 V91 F13.2 V92 F13.2 V93 F13.2 V94 F13.2 . CACHE. EXECUTE. MATCH FILES FILE=* /FILE= 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\CASELBL.SAV' . EXECUTE. FLIP VARIABLES= V50 TO V94 . 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'. 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'.