server-scripts/qhtcp-workflow/apps/matlab/ezview/EZmultiGeneRFsLst.m

% EZmultiGeneRFsLst  Called by EZmultiExLoad
% Called by EZmultiExLoad about line173 Which is called by EZexpSel
% User Select Reference Gene and Specifics Added

% Compile GeneList and OrfList
% Sort and add the medians of Ref Plates if RF1,RF2 exist
clear aa bb c uu vv drf drfPindx drfr drfc
clear RF1scanN RF2scanN

for mx=1:length(Exp(expN).Dexp(n).MP)
  try
  char((Exp(expN).Dexp(n).MP(mx).genename{1}(384)))      
  MPnum=mx;
  catch
    break
  end
end

DMnum=length(Exp(expN).Dexp(n).DM.drug);
tPtsSize=size(Exp(expN).Dexp(n).FexpScanBMtp{1,1},(3)); %size(FexpScanBMtp{1,1},3);
lstindx=0;
lstindxOrf=0;
spN=0;             
Exp(expN).Dexp(n).RFrnames  %<--???
rfcnt=0;
dRF1indx=0;
RF1mp=[];  RF2mp=[];
rfSp=cell2mat(rfSpec); % user entry of Specifics for Ref selection

for mp=1:MPnum 
  % RF1fullPlate=0;
  for ind384=1:384   
    spN=spN+1;
    try
      r=ceil(ind384/24); 
      if rem(ind384,24)==0, c=24; else c=rem(ind384,24); end
      % Insert test for numeric in genename and orf if isnumeric
      % Correct common EXCEL problem of converting OCT1 into a date numeric
      if cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))==38991,
        Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={'OCT1_'}; 
      elseif isnumeric(cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)))
        Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={' '}; 
      end
      %****Check for full(384spot) Reference Plates (RF1 or/and RF2)**************          
      RF1fullPlate=0;
      try RF1fullPlate=sum(ismember((Exp(expN).Dexp(n).MP(mp).genename{1}),rfGene))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
      RF2fullPlate=0;
      try RF2fullPlate=sum(ismember((Exp(expN).Dexp(n).MP(mp).genename{1}),'RF2'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
      % Capture non-reference spot location and ORF data       
      if isempty(regexpi(char((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384))),'blank'))...     %'\<blank\>'
      && ~isnumeric(Exp(expN).Dexp(n).MP(mp).orf{1}(ind384))...
      && ~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),' ')...
      && ~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),'  ')...
      && ~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),'')...
      && ~isempty((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)))...
      && ((~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene)|| ~strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),rfSp))... 
      && (~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene)|| ~strcmpi(rfSp,'None')))...
      && ((~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),rfGene)|| ~strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),rfSp))...
      && (~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),rfGene)|| ~strcmpi(rfSp,'None')))...
      && (~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),'RF2')||~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),'RF2'))... 
      && iscellstr((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)))
        lstindxOrf=lstindxOrf+1;
        Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)=strrep((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),':',' ');
        bb(lstindxOrf,1)=(Exp(expN).Dexp(n).MP(mp).orf{1}(ind384));
        bb(lstindxOrf,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
        bb(lstindxOrf,3)={mp};
        bb(lstindxOrf,4)={r};
        bb(lstindxOrf,5)={c};
        mutorfs(lstindxOrf)=spN;  %16_0318 added for Interaction EZinteract
        % Exp(expN).Dexp(n).mutSpotIndx(lstindxOrf)=spN;  %16_0318 added for Interaction EZinteract
      end    

      % Capture non-reference spot location and GENENAME data       
      if isempty(regexpi(char((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))),'blank'))...  %'\<blank\>'  
      && ~isnumeric(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))...
      && ~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),' ')...
      && ~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),'  ')...
      && ~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),'')...
      && ~isempty((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)))...
      && (~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene)...
      || ~strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),rfSp))...  % AddSpecifics rfSp && ~RF1fullPlate)...
      && (~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene) || ~strcmpi(rfSp,'None'))...
      && (~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),'RF2'))...  % && ~RF2fullPlate)...
      && iscellstr((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)))
        lstindx=lstindx+1;
        Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)=strrep((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),':',' ');
        aa(lstindx,1)=(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384));
        aa(lstindx,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};  
        aa(lstindx,3)={mp};
        aa(lstindx,4)={r};
        aa(lstindx,5)={c};
        mutgenes(lstindx)=spN;
      elseif (RF1fullPlate==1 ...   % sum(ismember((Exp(expN).Dexp(n).MP(mp).genename{1}),rfGene))==384 || ...
      || (((length(unique(Exp(expN).Dexp(n).MP(mp).genename{1}(1:384))))==1 && mp==1 ) ...   % (isequal((Exp(expN).Dexp(n).MP(mp).genename{1}(1:384)), (Exp(expN).Dexp(n).MP(mp).genename{1}(384:-1:1)))&& mp==1 )) && ...
      && ~exist('RF1scanN','var'))) 
        RF1mp=mp
        RF1scanN=(mp*DMnum)-(DMnum-1)
        rfcnt=rfcnt+1;
        RFs(spN:spN+383)=spN:spN+383;    
      elseif (RF2fullPlate==1|| ... % sum(ismember((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),'RF2'))==384 ||... 
        (((length(unique(Exp(expN).Dexp(n).MP(mp).genename{1}(1:384))))==1 && mp==MPnum ) && ... 
        ~exist('RF2scanN','var')))
        RF2mp=mp 
        rfcnt=rfcnt+1;
        RFs(spN:spN+383)=spN:spN+383;                          
        RF2scanN=(mp*DMnum)-(DMnum-1)

      % DISPersed REFerence capture and find Medians                
      elseif ( ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene) ...
      && strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),rfSp))) ...
      || ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene) ...
      && strcmpi(rfSp,'None'))) ) &&(RF1fullPlate~=1)
        dRF1indx=dRF1indx+1;
        Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)=strrep((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),':',' ');
        drf(dRF1indx,1)=(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384));
        drf(dRF1indx,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};  
        drf(dRF1indx,3)={mp}; drfMP(dRF1indx,mp)=mp;
        drf(dRF1indx,4)={r};  drfr(dRF1indx,mp)=r;
        drf(dRF1indx,5)={c};  drfc(dRF1indx,mp)=c;
        drf(dRF1indx,6)={ind384}; drfPindx(dRF1indx,mp)=ind384;
        % drf(dRF1indx,7)=(Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384));
      end   % if isempty(regexpi(char((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))),'blank'))...  
    catch
      mp % Disable in future to prevent a bomb out OR put into a nested TryCatch
      ind384 % Disable in future to prevent a bomb out OR put into a nested TryCatch
      msgBadGeneName=strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
    end
  end  
  mp 
end

% Cover case if mutorfs RFs are labeled RF1 or RF2
try
  Exp(expN).Dexp(n).mutSpotIndx.wRFs=union(RFs, mutorfs);
catch
  msg='No RFs Found in Exp! wRFs'
  Exp(expN).Dexp(n).mutSpotIndx.wRFs=mutorfs;
end
try
  Exp(expN).Dexp(n).mutSpotIndx.woRFs=setdiff(mutorfs,RFs);
catch
  msg='No RFs Found in Exp! woRFs'
  Exp(expN).Dexp(n).mutSpotIndx.woRFs=mutorfs;
end
   
Exp(expN).Dexp(n).RFmd1indx=[];
Exp(expN).Dexp(n).RFmd1pltN=[];
Exp(expN).Dexp(n).RFmd1LB={[]};
Exp(expN).Dexp(n).RFmd1indx=[];
Exp(expN).Dexp(n).RFmd1pltN={}; 
Exp(expN).Dexp(n).RFmd1val=[];
Exp(expN).Dexp(n).mean1=[]; 
Exp(expN).Dexp(n).std1=[];
Exp(expN).Dexp(n).min1=[];
Exp(expN).Dexp(n).max1=[];

Exp(expN).Dexp(n).RFcmpK=[]; %For Ref Composite 17_1009 
Exp(expN).Dexp(n).RFcmpr=[]; %For Ref Composite 17_1009 
Exp(expN).Dexp(n).RFcmpL=[]; %For Ref Composite 17_1009 

Exp(expN).Dexp(n).RFmd2LB={[]};
Exp(expN).Dexp(n).RFmd2indx=[];
Exp(expN).Dexp(n).RFmd2pltN=[];
Exp(expN).Dexp(n).RFmd2val=[];
Exp(expN).Dexp(n).mean2=[];
Exp(expN).Dexp(n).std2=[];
Exp(expN).Dexp(n).min2=[];
Exp(expN).Dexp(n).max2=[];

Exp(expN).Dexp(n).RFmean=[];
Exp(expN).Dexp(n).RFstd=[];
Exp(expN).Dexp(n).RFmin=[];
Exp(expN).Dexp(n).RFmax=[];

Exp(expN).Dexp(n).RFmdPLB={[]};
Exp(expN).Dexp(n).RFmdPindx=[];
Exp(expN).Dexp(n).RFmdPpltN=[];
Exp(expN).Dexp(n).RFmdPscanN=[];
Exp(expN).Dexp(n).RFmedianP=[];
Exp(expN).Dexp(n).stdP=[];
Exp(expN).Dexp(n).meanP=[];
Exp(expN).Dexp(n).minP=[];
Exp(expN).Dexp(n).maxP=[];

Exp(expN).Dexp(n).RFmdGLB={[]};
Exp(expN).Dexp(n).RFmdGindx=[];
Exp(expN).Dexp(n).RFmdGpltN=[];
Exp(expN).Dexp(n).RFmdGscanN=[];
Exp(expN).Dexp(n).RFmedianG=[];
Exp(expN).Dexp(n).RFminG=[];
Exp(expN).Dexp(n).RFmaxG=[];
Exp(expN).Dexp(n).RFstdG=[];
Exp(expN).Dexp(n).RFmeanG=[];
Exp(expN).Dexp(n).RFcmpGK=[]; %For Ref Composite 17_1009 
Exp(expN).Dexp(n).RFcmpGr=[]; %For Ref Composite 17_1009 
Exp(expN).Dexp(n).RFcmpGL=[]; %For Ref Composite 17_1009 

if exist('RF1scanN','var')     
  for d=0:(DMnum-1)
    medianIndx=[];
    nonZeroIndx=[];
    medValList=[];
    rf1scN=RF1scanN+d;

    try  %if RF1scanN doesn't exist this addition to list will be skipped
      nonZeroIndx=find(Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(1:384,5));
      
      if isempty(nonZeroIndx)
        nonZeroCnt=0
        medianIndx=nonZeroIndx; 
      else 
        nonZeroCnt=length(nonZeroIndx); 
      end
      if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)==0, medianIndx=nonZeroIndx(1:nonZeroCnt-1); end
      if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)~=0, medianIndx=nonZeroIndx; end 
      clear medValLst   
      clear kValLst
      clear rValLst
      if ~isempty(nonZeroIndx) && length(medianIndx) > (.15*384) % To calc. a median, more than 15% of spots must be nonZero
        medValLst=Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(medianIndx,5);
        medValList1{d+1}=medValLst;
        min1=min(medValLst);
        max1=max(medValLst);
        std1=std(medValLst);
        mean1=mean(medValLst);
        kValLst=Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(medianIndx,3); % For Ref Composite 17_1009
        rValLst=Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(medianIndx,4); % For Ref Composite 17_1009
        mval1=median(medValLst);  %mval1=median(Exp(expN).Dexp(n).scan(RF1mps).plate(1).CFout(1:384,5));  %CFout(1:383,5));
        RFmd1pos=find(mval1==(Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(1:384,5)));
        RFmd1loc(1)=ceil(RFmd1pos/24); %calc r value
        RFmd1loc(2)=RFmd1pos - ((RFmd1loc(1)-1)*24);  %calc c value
        lstindx=lstindx+1;
        lstindxOrf=lstindxOrf+1;
        aa(lstindx,1)={strcat('RF1md(',num2str(d+1),')')};  %{'RF1md'};
        aa(lstindx,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))};    %,'std_',num2str(std1))};
        bb(lstindxOrf,1)={strcat('RF1md(',num2str(d+1),')')};  %remove string2cell brackets {...} %{'RF1md'};
        bb(lstindxOrf,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))};  %,'std_',num2str(std1))};
        % Composite Reference Amalgum Plot
        lstindx=lstindx+1;
        lstindxOrf=lstindxOrf+1;
        aa(lstindx,1)={strcat('RF1cmp(',num2str(d+1),')')}; 
        aa(lstindx,2)={''};
        bb(lstindxOrf,1)={strcat('RF1cmp(',num2str(d+1),')')};
        bb(lstindxOrf,2)={''};

        Exp(expN).Dexp(n).RFmd1LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2));
        Exp(expN).Dexp(n).RFmd1indx(d+1)=RFmd1pos;
        Exp(expN).Dexp(n).RFmd1pltN=RF1mp;
        Exp(expN).Dexp(n).RFmd1val(d+1)=mval1;
        Exp(expN).Dexp(n).mean1(d+1)=mean1; 
        Exp(expN).Dexp(n).std1(d+1)=std1;
        Exp(expN).Dexp(n).min1(d+1)=min1;
        Exp(expN).Dexp(n).max1(d+1)=max1;
        Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).Lvals=medValLst;  %17_1201 TrendOL
        Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).med=median(medValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).mean=mean(medValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).std=std(medValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).min=min(medValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).max=max(medValLst); %For Ref Composite 17_1009
        Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).Kvals=kValLst;
        Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).med=median(kValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).mean=mean(kValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).std=std(kValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).min=min(kValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).max=max(kValLst); %For Ref Composite 17_1009
        Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).rvals=rValLst;
        Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).med=median(rValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).mean=mean(rValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).std=std(rValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).min=min(rValLst); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).max=max(rValLst); %For Ref Composite 17_1009 
      else
        % Need to set L r K values to zeros or pick the first spot with zeros
        % Spot 1 could be other than zero as the median isn't calculated if
        % fewer than some percent are nonzero
        medianCalcFailed='To Few nonZero spots for valid median RF1 selection' 
        firstZero=find(((Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first') 
        Exp(expN).Dexp(n).RFmd1indx(d+1)=firstZero; 
        Exp(expN).Dexp(n).RFmd1pltN=RF1mp; 
        try medValList1{d+1}=Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(medianIndx,5); nonZeroCnt; catch, catcherror='Ln356', end
      end
    catch
      medianCalcTryFailed1='Failed! Failed! Ln362 But process continued with placeholder P1ind384 spot value!'
      try
        firstZero=find(((Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first')  
        Exp(expN).Dexp(n).RFmd1indx(d+1)=firstZero;
      catch
        Exp(expN).Dexp(n).RFmd1indx(d+1)=384; %if crapout,Then use spot384 as default to keep going  
      end
      try
        Exp(expN).Dexp(n).RFmd1pltN=RF1mp;  
      catch
        Exp(expN).Dexp(n).RFmd1pltN=1; 
      end
    end
  end
end

% Calc RF2 median if a full plate of RF2s exist
Exp(expN).Dexp(n).RFmd2indx=[];
Exp(expN).Dexp(n).RFmd2pltN=[];

if exist('RF2scanN','var')  
  for d=0:(DMnum-1)
    medianIndx2=[];
    nonZeroIndx2=[];
    medValList2=[];
    rf2scN=RF2scanN+d;
    
    try  %if RF2scanN doesn't exist this addition to list will be skipped  
      nonZeroIndx2=find(Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(1:384,5));
      if isempty(nonZeroIndx2)
        nonZeroCnt2=0;
        medianIndx2=nonZeroIndx2; 
      else 
        nonZeroCnt2=length(nonZeroIndx2); 
      end
      if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)==0, medianIndx2=nonZeroIndx2(1:nonZeroCnt2-1); end
      if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)~=0, medianIndx2=nonZeroIndx2; end    
      clear medValLst2   
      clear kValLst2
      clear rValLst2
      if ~isempty(nonZeroIndx2) && length(medianIndx2) > (.15*384) % to calc. a median, more than 15% of spots must be nonZero   
        medValLst2=Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(medianIndx2,5);
        medValList2{d+1}=medValLst2;
        min2=min(medValLst2);
        max2=max(medValLst2);
        std2=std(medValLst2);
        mean2=mean(medValLst2);
        kValLst2=Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(medianIndx2,3); %For Ref Composite 17_1009
        rValLst2=Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(medianIndx2,4); %For Ref Composite 17_1009    
        mval2=median(medValLst2);  %mval2=median(Exp(expN).Dexp(n).scan(RF2mps).plate(1).CFout(1:383,5));
        RFmd2pos=find(mval2==(Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(1:384,5)));
        RFmd2loc(1)=ceil(RFmd2pos/24); %calc r value
        RFmd2loc(2)=RFmd2pos - ((RFmd2loc(1)-1)*24);  %calc c value
        lstindx=lstindx+1;
        lstindxOrf=lstindxOrf+1;
        aa(lstindx,1)={strcat('RF2md(',num2str(d+1),')')};     %{'RF2md'}; 
        aa(lstindx,2)={strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))};  %,'std_',num2str(std2))};
        bb(lstindxOrf,1)={strcat('RF2md(',num2str(d+1),')')};  %remove string2cell brackets {...}  %{'RF2md'};
        bb(lstindxOrf,2)={strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))};  %,'std_',num2str(std2))};
        % Composite Reference Amalgum Plot   (CRAP)
        lstindx=lstindx+1;
        lstindxOrf=lstindxOrf+1;
        aa(lstindx,1)={strcat('RF2cmp(',num2str(d+1),')')}; 
        aa(lstindx,2)={''};
        bb(lstindxOrf,1)={strcat('RF2cmp(',num2str(d+1),')')}; 
        bb(lstindxOrf,2)={''};

        Exp(expN).Dexp(n).RFmd2LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2));
        Exp(expN).Dexp(n).RFmd2indx(d+1)=RFmd2pos;
        Exp(expN).Dexp(n).RFmd2pltN=RF2mp;
        Exp(expN).Dexp(n).RFmd2val(d+1)=mval2;
        Exp(expN).Dexp(n).mean2(d+1)=mean2;
        Exp(expN).Dexp(n).std2(d+1)=std2;
        Exp(expN).Dexp(n).min2(d+1)=min2;
        Exp(expN).Dexp(n).max2(d+1)=max2;
        Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).Lvals=medValLst2;  %17_1201 TrendOL
        Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).med=median(medValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).mean=mean(medValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).std=std(medValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).min=min(medValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).max=max(medValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).Kvals=kValLst2;
        Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).med=median(kValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).mean=mean(kValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).std=std(kValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).min=min(kValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).max=max(kValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).rvals=rValLst2;
        Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).med=median(rValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).mean=mean(rValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).std=std(rValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).min=min(rValLst2); %For Ref Composite 17_1009 
        Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).max=max(rValLst); %For Ref Composite 17_1009 
      else
        % Pick the first spot with zeros
        % Use that position to satisfy and keep process OK
        medianCalcFailed2='To Few nonZero spots for valid median RF2 selection'
        firstZero2=find(((Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first')   
        Exp(expN).Dexp(n).RFmd2indx(d+1)=firstZero2; 
        Exp(expN).Dexp(n).RFmd2pltN=RF2mp; 
        try medValList2{d+1}=Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(medianIndx2,5);  nonZeroCnt2; catch, catchissue='Ln431', end
      end
    catch
      medianCalcTryFailed2='Failed! Failed! Ln436 No RF1median But process continued with placeholder P1ind384 spot value!'
      try
        firstZero2=find(((Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first');
        Exp(expN).Dexp(n).RFmd2indx(d+1)=firstZero2;
      catch
        catchissue='Ln442'
        Exp(expN).Dexp(n).RFmd2indx(d+1)=384;  %if crapout,Then use spot384 as default to keep going  
      end
      try
        Exp(expN).Dexp(n).RFmd2pltN=RF2mp; 
      catch
        catchissue='Ln448'
        Exp(expN).Dexp(n).RFmd2pltN=1;
      end
    end
    clear RFcombValList
    RFcombValList=cat(1,medValList1{d+1},medValList2{d+1});
    Exp(expN).Dexp(n).RFmean(d+1)=mean(RFcombValList);
    Exp(expN).Dexp(n).RFstd(d+1)=std(RFcombValList);
    try, Exp(expN).Dexp(n).RFmin(d+1)=min(RFcombValList);
    catch, Exp(expN).Dexp(n).RFmin(d+1)=0; end
    try, Exp(expN).Dexp(n).RFmax(d+1)=max(RFcombValList);
    catch, Exp(expN).Dexp(n).RFmax(d+1)=0; end
  end
elseif exist('RF1scanN','var')
  Exp(expN).Dexp(n).RFmean=Exp(expN).Dexp(n).mean1;
  Exp(expN).Dexp(n).RFstd=Exp(expN).Dexp(n).std1;
  Exp(expN).Dexp(n).RFmin=Exp(expN).Dexp(n).min1;
  Exp(expN).Dexp(n).RFmax=Exp(expN).Dexp(n).max1;
end  

% Disperse reference plates
Exp(expN).Dexp(n).RFmdPindx=[];
Exp(expN).Dexp(n).RFmdPpltN=[];
if exist('drf','var') % ('RF1scanN','var') 
  % Det. index of change from one MP to the next    
  i=2;
  clear chgIndx
  chgIndx(1)=1;
  for j=1:length(drf(:,3))
    if j>1
      if cell2mat(drf(j,3))~=cell2mat(drf((j-1),3)), chgIndx(i)=j; i=i+1; end
    end
  end
  chgIndx(length(chgIndx)+1)=length(drf)+1;
  uu=zeros(size(drf,1),4);
  uu(:,1:4)=cell2mat(drf(:,3:6));
  vv=zeros(size(drf,1),DMnum);   %(length(drf),DMnum);
  dMPs=unique(cell2mat(drf(:,3))); 
  %{
  for mm=1:MPnum
      nonZrfIndx.mp{mm,:}=drfPindx((find(drfPindx(:,mm))),mm);
  end
  %}
  % nzValsG=zeros(DMnum,size(drf,1));
  % nzValsAcc=zeros(DMnum,384);
  for mm=1:length(dMPs) % length(chgIndx)
    for d=1:(DMnum)
      medianIndxDisp=[];
      NZrefIndxP=[];
      nonZeroValsP=[];
      medValLstDisp=[];
      rf1scNdisp=((dMPs(mm)-1)*DMnum)+(d);

      % Determine the dispersed RFs median mean and std if such exist
      try  
        NZrefIndxP=drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm));   % find(Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(drf(chgIndx(cI):chgIndx(cI+1)),5));
        % vv=Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
        vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
        % For Global Ref Composite 17_1009 
        vvK(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,3);
        vvr(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,4);
        nonZeroValsP=nonzeros(Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
        std1Disp=std(nonZeroValsP);
        mean1Disp=mean(nonZeroValsP);
        minDisp=min(nonZeroValsP);
        maxDisp=max(nonZeroValsP);
        drfVals=Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
        % nzValsAcc(mm).DM(d,:)=nonZeroValsP;
        % MEDIAN Determination for PLATES with Dispersed RFs
        % NZrefIndxP=NZrefIndxP %find(Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
        if isempty(NZrefIndxP)
          nonZeroCntDisp=0;
          medianIndxDisp=NZrefIndxP; 
        else
          nonZeroCntDisp=length(NZrefIndxP); 
        end
                                    
        if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)==0, medianIndxDisp=NZrefIndxP(1:nonZeroCntDisp-1); end
        if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)~=0, medianIndxDisp=NZrefIndxP; end 
        if ~isempty(NZrefIndxP) && length(medianIndxDisp) > 0 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
          medValLstDisp=Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(medianIndxDisp,5);
          %medValList1Disp{d}=medValLstDisp;
          mval1Disp=median(medValLstDisp);  % mval1=median(Exp(expN).Dexp(n).scan(RF1mps).plate(1).CFout(1:384,5));  %CFout(1:383,5));
          nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP);  % (Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5)));  %(nonZeroIndxDisp,5)));   %((nonZrfIndx.mp{dMPs(mm),:}),5)));
          RFmd1posD=NZrefIndxP(nonZeroMedPosIndx);  % drfPindx((RFmd1posIndx),dMPs(mm));
          RFmd1locD(1)=ceil(RFmd1posD/24); % calc r value
          RFmd1locD(2)=RFmd1posD - ((RFmd1locD(1)-1)*24);  % calc c value
          lstindx=lstindx+1;
          lstindxOrf=lstindxOrf+1;
          if usrRefFg==0, rfPLbl='RF1mdP('; else rfPLbl=strcat('RF-',rfGnSp,'mdP('); end  % accomodate User Ref Selection
          if iscell(strcat(rfPLbl,num2str(d),')')), 
            aa(lstindx,1)=strcat(rfPLbl,num2str(d),')');
            bb(lstindxOrf,1)=strcat(rfPLbl,num2str(d),')'); % remove string2cell brackets {...}
          else 
            aa(lstindx,1)={strcat(rfPLbl,num2str(d),')')};
            bb(lstindxOrf,1)={strcat(rfPLbl,num2str(d),')')};   %remove string2cell brackets {...}
          end
          aa(lstindx,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};  
          bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
          Exp(expN).Dexp(n).RFmdPLB(d,dMPs(mm))=strcat(aa(lstindx,1),aa(lstindx,2));
          Exp(expN).Dexp(n).RFmdPindx(d,dMPs(mm))=RFmd1posD;
          Exp(expN).Dexp(n).RFmdPpltN(d,dMPs(mm))=dMPs(mm);   %This is a storage of the MasterPlate used NOT the ScanPlate?  WeMight wish to store the ScanPlateNumber also???
          Exp(expN).Dexp(n).RFmdPscanN(d,dMPs(mm))=rf1scNdisp;
          Exp(expN).Dexp(n).RFmedianP(d,dMPs(mm))=mval1Disp;
          Exp(expN).Dexp(n).stdP(d,dMPs(mm))=std1Disp;
          Exp(expN).Dexp(n).meanP(d,dMPs(mm))=mean1Disp; 
          Exp(expN).Dexp(n).minP(d,dMPs(mm))=minDisp;
          Exp(expN).Dexp(n).maxP(d,dMPs(mm))=maxDisp;
        else
          % Need to set L r K values to zeros or pick the first spot with zeros
          % Spot 1 could be other than zero as the median isn't calculated if fewer than some percent are nonzero
          medianCalcFailedD='To Few nonZero spots for valid median RF1 selection' 
          firstZeroDindx=find(((Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
          firstZeroD=drfPindx((firstZeroDindx),dMPs(mm));
          Exp(expN).Dexp(n).RFmdPindx(d,dMPs(mm))=firstZeroD; 
          Exp(expN).Dexp(n).RFmdPpltN(d,dMPs(mm))=dMPs(mm); % RF1mp;  % Is this supposed to be the MP number or the ScanPlate number???
        end
      catch
        medianCalcTryFailed1D='Failed! Failed! Ln565 {Dispersed RF1s} "try" But process continued with placeholder Plate spot value!'
        try
          firstZeroindxD=find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first'); 
          firstZeroPindx=uu(firstZeroindxD,4);
          Exp(expN).Dexp(n).RFmdPpltN(d,dMPs(mm))=dMPs(mm);
          Exp(expN).Dexp(n).RFmdPindx(d,dMPs(mm))=firstZeroPindx;
        catch
          catchissue='try at Ln565'
          Exp(expN).Dexp(n).RFmdPpltN(d,dMPs(mm))=dMPs(mm);
          Exp(expN).Dexp(n).RFmdPindx(d,dMPs(mm))=384; % if crapout,Then use spot384 as default to keep going  
        end
        try
          Exp(expN).Dexp(n).RFmdPpltN=dMPs(mm);  
        catch
          catchissue='Ln619'
          Exp(expN).Dexp(n).RFmdPpltN=1;  % this might keep from breaking BUT ??? 
        end
      end
    end
  end

  % Calc. Global Mean, Std, And Median For Distributed References
  uu=horzcat(uu,vv);
  for d=1:DMnum
    medianIndxG=[];
    NZrfIndxG=[];
    minG=min(nonzeros(vv(:,d)));
    maxG=max(nonzeros(vv(:,d)));
    RFmeanG=mean(nonzeros(vv(:,d)));
    RFstdG=std(nonzeros(vv(:,d)));
    NZrfIndxG=find(vv(:,d)); % find(nonzeros(vv(:,d)));
  
    if isempty(RFmeanG)
      nonZeroCntD=0 % medianIndxDisp=RFmeanG(d); 
    else 
      nonZeroCntD=length(nonzeros(vv(:,d))); 
    end

    % Calc. of median requires an odd number of indx items 
    if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)==0, medianIndxD=NZrfIndxG(1:(size(NZrfIndxG,1)-1)); end
    if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)~=0, medianIndxD=NZrfIndxG(:); end 
    if ~isempty(NZrfIndxG) && length(medianIndxD) > 0 %(.15*size(drf,1)) % to calc. a median, more than 15% of spots must be nonZero 
      mvalsDG=median(vv(medianIndxD,d)); % (nonzeros(vv(:,d))); 
      nzPosIndxDG=find(mvalsDG==vv(:,d)); 
      RFmdDGloc(d,1)=uu(nzPosIndxDG,1);  % MP of distributedGlobal Median value
      RFmdDGloc(d,2)=uu(nzPosIndxDG,2);  % calc r value
      RFmdDGloc(d,3)=uu(nzPosIndxDG,3);  % calc c value
      lstindx=lstindx+1;
      lstindxOrf=lstindxOrf+1;
      if usrRefFg==0, rfGLbl='RF1mdG('; else rfGLbl=strcat('RF-',rfGnSp,'mdG('); end  %accomodate User Ref Selection
      if iscell(strcat(rfPLbl,num2str(d),')')), 
        aa(lstindx,1)=strcat(rfGLbl,num2str(d),')');  % remove string2cell brackets {...}
        bb(lstindxOrf,1)=strcat(rfGLbl,num2str(d),')');  % remove string2cell brackets {...}
      else
        aa(lstindx,1)={strcat(rfGLbl,num2str(d),')')};  
        bb(lstindxOrf,1)={strcat(rfGLbl,num2str(d),')')};     
      end
      aa(lstindx,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))};  %,'std_',num2str(std2))};
      bb(lstindxOrf,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))};  %,'std_',num2str(std2))};
      % Composite Reference Amalgum Plot
      lstindx=lstindx+1;
      lstindxOrf=lstindxOrf+1;
      if usrRefFg==0, rfcmpGLbl='RFcmpG('; else rfcmpGLbl=strcat('RFcmpG-',rfGnSp,'('); end  %accomodate User Ref Selection
      if iscell(strcat(rfcmpGLbl,num2str(d),')')), 
        aa(lstindx,1)=strcat(rfcmpGLbl,num2str(d),')'); % strcat('RFcmpG(',num2str(d),')'); 
        bb(lstindxOrf,1)=strcat(rfcmpGLbl,num2str(d),')'); % strcat('RFcmpG(',num2str(d),')');
      else
        aa(lstindx,1)={strcat(rfcmpGLbl,num2str(d),')')}; 
        bb(lstindxOrf,1)={strcat(rfcmpGLbl,num2str(d),')')};
      end

      aa(lstindx,2)={''};
      bb(lstindxOrf,2)={''};
      Exp(expN).Dexp(n).RFmdGLB(d)=strcat(aa(lstindx,1),aa(lstindx,2));
      Exp(expN).Dexp(n).RFmdGindx(d)=nzPosIndxDG;
      Exp(expN).Dexp(n).RFmdGpltN(d)=RFmdDGloc(d,1);  
      Exp(expN).Dexp(n).RFmdGscanN(d)=uu(nzPosIndxDG,4);
      Exp(expN).Dexp(n).RFmedianG(d)=mvalsDG;
      Exp(expN).Dexp(n).RFminG(d)=minG;
      Exp(expN).Dexp(n).RFmaxG(d)=maxG;
      Exp(expN).Dexp(n).RFstdG(d)=RFstdG;
      Exp(expN).Dexp(n).RFmeanG(d)=RFmeanG; 
      Exp(expN).Dexp(n).RFcmpGL.dm(d).Lvals=vv(medianIndxD,d); %17_1201 TrendOL
      Exp(expN).Dexp(n).RFcmpGL.dm(d).med=median(vv(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGL.dm(d).mean=mean(vv(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGL.dm(d).std=std(vv(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGL.dm(d).min=min(vv(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGL.dm(d).max=max(vv(medianIndxD,d)); %For Ref Composite 17_1009
      Exp(expN).Dexp(n).RFcmpGK.dm(d).Kvals=vvK(medianIndxD,d); %17_1201 TrendOL
      Exp(expN).Dexp(n).RFcmpGK.dm(d).med=median(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGK.dm(d).mean=mean(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGK.dm(d).std=std(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGK.dm(d).min=min(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGK.dm(d).max=max(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGr.dm(d).rvals=vvr(medianIndxD,d); %17_1201 TrendOL
      Exp(expN).Dexp(n).RFcmpGr.dm(d).med=median(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGr.dm(d).mean=mean(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGr.dm(d).std=std(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGr.dm(d).min=min(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
      Exp(expN).Dexp(n).RFcmpGr.dm(d).max=max(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
    end
  end  
end 

% EZusrSelRef
gnLstRaw=strcat(aa(:,1),aa(:,2));
Exp(expN).Dexp(n).srtGnLst=sort(gnLstRaw);

orfLstRaw=strcat(bb(:,1),bb(:,2));
Exp(expN).Dexp(n).srtOrfLst=sort(orfLstRaw);

%{
%set(handles.MPsldr2,'max',length(MP));
%set(handles.DMsldr2,'max',length(DM.drug));
%set(handles.Tptsldr2,'max',tPtsSize);

%set(handles.MPsldr2,'min',1,'max',MPnum)

%set(handles.DMsldr2,'min',1,'max',DMnum)  
%tPtsSize=size(Exp(expN).Dexp(n).FexpScanBMtp{1,1},(3));
%set(handles.Tptsldr2,'min',1,'max',tPtsSize)

%set(handles.MPsldr2,'value',1)
%set(handles.DMsldr2,'value',1)
%set(handles.Tptsldr2,'value',1)
%set(handles.MPed2,'string','1')
%set(handles.DMed2,'string','1')
%set(handles.Tpted2,'string','1')
%set(handles.MPsldr2,'SliderStep',[1/length(MP) 1/length(MP)]);
%set(handles.DMsldr2,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
%set(handles.Tptsldr2,'SliderStep',[1/tPtsSize 1/tPtsSize]);
%}