% 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'))... %'\' && ~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'))... %'\' && ~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]); %}