200 lines
9.4 KiB
Matlab
Executable File
200 lines
9.4 KiB
Matlab
Executable File
%EZusrSelRef
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% User Select Reference Diaglog Box
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try
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if n==1 && ~exist('RF1scanN','var') && ~exist('RF2scanN','var') %change || &&
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%{
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prompt={'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
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'Enter GeneName of Your Reference:'};
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rfMPstr=cell2mat(answer(1));
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rfMPcomas=strfind((cell2mat(answer(1))),',');
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n=0;
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if isempty(rfMPcomas)|| max(rfMPcomas)==length(rfMPstr)
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usrMPs=rfMPstr
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else
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for i=rfMPcomas,
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n=n+1
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usrMPs(n)=str2double(rfMPstr(i-1:i))
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if i==max(rfMPcomas)
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usrMPs(n+1)=str2double(rfMPstr(i:end))
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end
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end
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end
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usrMPs=answer(1);
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refGene=answer(2);
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%}
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prompt={'Enter GeneName to use as Reference:',...
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'Enter Specifics Term if used to futher specify Reference '}
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dlg_title='User Reference Input';
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num_lines=1;
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def={'None','Specifics Term'};
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answer=inputdlg(prompt,dlg_title,num_lines,def);
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rfGenestr=cell2mat(answer(1));
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rfSpec=cell2mat(answer(2));
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end
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%try
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for mp=1:length(Exp(expN).Dexp(DexpN).MP)
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for ind384=1:384
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spN=spN+1;
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end
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%catch
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%end %try for user selected Reference routine
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end
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% Disperse Reference Plates
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Exp(expN).Dexp(DexpN).RFmdPindx=[];
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Exp(expN).Dexp(DexpN).RFmdPpltN=[];
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if exist('drf','var') % ('RF1scanN','var')
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%Det. index of change from one MP to the next
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i=2;
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chgIndx(1)=1;
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for j=1:length(drf(:,3))
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if j>1
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if cell2mat(drf(j,3))~=cell2mat(drf((j-1),3)), chgIndx(i)=j; i=i+1; end
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end
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end
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chgIndx(length(chgIndx)+1)=length(drf)+1;
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uu=zeros(size(drf,1),4);
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uu(:,1:4)=cell2mat(drf(:,3:6))
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vv=zeros(length(drf),DMnum);
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dMPs=unique(cell2mat(drf(:,3)));
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%{
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for mm=1:MPnum
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nonZrfIndx.mp{mm,:}=drfPindx((find(drfPindx(:,mm))),mm);
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end
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%}
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% nzValsG=zeros(DMnum,size(drf,1));
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% nzValsAcc=zeros(DMnum,384);
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for mm=1:length(dMPs) % length(chgIndx)
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for d=1:(DMnum)
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medianIndxDisp=[];
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NZrefIndxP=[];
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nonZeroValsP=[];
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medValLstDisp=[];
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rf1scNdisp=((dMPs(mm)-1)*DMnum)+(d);
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try % Determine the dispersed RFs median mean and std if such exist
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NZrefIndxP=drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); %find(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(drf(chgIndx(cI):chgIndx(cI+1)),5));
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% vv=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
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vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
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nonZeroValsP=nonzeros(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
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std1Disp=std(nonZeroValsP);
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mean1Disp=mean(nonZeroValsP);
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minDisp=min(nonZeroValsP);
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maxDisp=max(nonZeroValsP);
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drfVals=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
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%nzValsAcc(mm).DM(d,:)=nonZeroValsP;
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%MEDIAN Determination for PLATES with Dispersed RFs
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%NZrefIndxP=NZrefIndxP %find(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
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if isempty(NZrefIndxP)
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nonZeroCntDisp=0
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medianIndxDisp=NZrefIndxP;
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else
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nonZeroCntDisp=length(NZrefIndxP);
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end
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if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)==0, medianIndxDisp=NZrefIndxP(1:nonZeroCntDisp-1); end
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if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)~=0, medianIndxDisp=NZrefIndxP; end
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if ~isempty(NZrefIndxP) && length(medianIndxDisp) > 3 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
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medValLstDisp=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(medianIndxDisp,5);
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%medValList1Disp{d}=medValLstDisp;
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mval1Disp=median(medValLstDisp); %mval1=median(Exp(expN).Dexp(DexpN).scan(RF1mps).plate(1).CFout(1:384,5)); %CFout(1:383,5));
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nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP); %(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))); %(nonZeroIndxDisp,5))); %((nonZrfIndx.mp{dMPs(mm),:}),5)));
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RFmd1posD=NZrefIndxP(nonZeroMedPosIndx); %drfPindx((RFmd1posIndx),dMPs(mm));
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RFmd1locD(1)=ceil(RFmd1posD/24); %calc r value
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RFmd1locD(2)=RFmd1posD - ((RFmd1locD(1)-1)*24); %calc c value
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lstindx=lstindx+1;
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lstindxOrf=lstindxOrf+1;
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aa(lstindx,1)={strcat('RF1mdP(',num2str(d),')')};
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aa(lstindx,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
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bb(lstindxOrf,1)={strcat('RF1mdP(',num2str(d),')')};
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bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
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Exp(expN).Dexp(DexpN).RFmdPLB(d,dMPs(mm))=strcat(aa(lstindx,1),aa(lstindx,2));
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Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=RFmd1posD;
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Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))=dMPs(mm); %This is a storage of the MasterPlate used NOT the ScanPlate? WeMight wish to store the ScanPlateNumber also???
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Exp(expN).Dexp(DexpN).RFmdPscanN(d,dMPs(mm))=rf1scNdisp;
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Exp(expN).Dexp(DexpN).RFmedianP(d,dMPs(mm))=mval1Disp;
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Exp(expN).Dexp(DexpN).stdP(d,dMPs(mm))=std1Disp;
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Exp(expN).Dexp(DexpN).meanP(d,dMPs(mm))=mean1Disp;
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Exp(expN).Dexp(DexpN).minP(d,dMPs(mm))=minDisp;
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Exp(expN).Dexp(DexpN).maxP(d,dMPs(mm))=maxDisp;
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else
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% Need to set L r K values to zeros or pick the first spot with zeros
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% Spot 1 could be other than zero as the median isn't calculated if fewer than some percent are nonzero
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medianCalcFailedD='To Few nonZero spots for valid median RF1 selection'
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firstZeroDindx=find(((Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
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firstZeroD=drfPindx((firstZeroDindx),dMPs(mm));
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Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=firstZeroD;
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Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))=dMPs(mm); %RF1mp; %Is this supposed to be the MP number or the ScanPlate number???
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end
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catch
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medianCalcTryFailed1D='Failed! Failed! Ln565 {Dispersed RF1s} "try" But process continued with bogus Plate spot value!'
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try
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firstZeroindxD=find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first');
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firstZeroPindx=uu(firstZeroindxD,4);
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Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))=dMPs(mm);
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Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=firstZeroPindx;
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catch
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Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))=dMPs(mm);
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Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=384; %if crapout,Then use spot384 as default to keep going
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end
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try
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Exp(expN).Dexp(DexpN).RFmdPpltN=dMPs(mm);
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catch
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Exp(expN).Dexp(DexpN).RFmdPpltN=1; %This might keep from breaking BUT ???
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end
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end
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end % for d=0:DMnum
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end % for mm=1:length(dMPs)
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% Calc. Global Mean, Std, And Median For Distributed References
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uu=horzcat(uu,vv);
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for d=1:DMnum
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medianIndxG=[];
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NZrfIndxG=[];
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minG=min(nonzeros(vv(:,d)));
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maxG=max(nonzeros(vv(:,d)));
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RFmeanG=mean(nonzeros(vv(:,d)));
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RFstdG=std(nonzeros(vv(:,d)));
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NZrfIndxG=find(nonzeros(vv(:,d)));
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if isempty(RFmeanG)
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nonZeroCntD=0
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% medianIndxDisp=RFmeanG(d);
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else
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nonZeroCntD=length(nonzeros(vv(:,d)));
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end
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% Calc. of median requires an odd number of indx items
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if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)==0, medianIndxD=NZrfIndxG(1:(size(NZrfIndxG,1)-1)); end
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if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)~=0, medianIndxD=NZrfIndxG(:); end
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if ~isempty(NZrfIndxG) && length(medianIndxD) > (.15*size(drf,1)) % To calc. a median, more than 15% of spots must be nonZero
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mvalsDG=median(vv(medianIndxD,d)); % (nonzeros(vv(:,d)));
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nzPosIndxDG=find(mvalsDG==vv(:,d));
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RFmdDGloc(d,1)=uu(nzPosIndxDG,1); % MP of distributedGlobal Median value
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RFmdDGloc(d,2)=uu(nzPosIndxDG,2); % calc r value
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RFmdDGloc(d,3)=uu(nzPosIndxDG,3); % calc c value
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lstindx=lstindx+1;
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lstindxOrf=lstindxOrf+1;
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aa(lstindx,1)={strcat('RF1mdG(',num2str(d),')')};
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aa(lstindx,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
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bb(lstindxOrf,1)={strcat('RF1mdG(',num2str(d),')')};
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bb(lstindxOrf,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
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Exp(expN).Dexp(DexpN).RFmdGLB(d)=strcat(aa(lstindx,1),aa(lstindx,2));
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Exp(expN).Dexp(DexpN).RFmdGindx(d)=nzPosIndxDG;
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Exp(expN).Dexp(DexpN).RFmdGpltN(d)=RFmdDGloc(d,1);
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Exp(expN).Dexp(DexpN).RFmdGscanN(d)=uu(nzPosIndxDG,4);
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Exp(expN).Dexp(DexpN).RFmedianG(d)=mvalsDG;
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Exp(expN).Dexp(DexpN).RFminG(d)=minG;
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Exp(expN).Dexp(DexpN).RFmaxG(d)=maxG;
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Exp(expN).Dexp(DexpN).RFstdG(d)=RFstdG;
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Exp(expN).Dexp(DexpN).RFmeanG(d)=RFmeanG;
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end
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end
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end
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catch
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msg='Failed attempt to apply User Selected Reference'
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end
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