%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) %mp; 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) %mp; %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 error='EZexpSel lineAfter 24 EZmultiGeneLst.m' 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 %end associated with for ind384=1:384 mp end %end associated with for mp=1:length(Exp(expN).Dexp(n).MP) %***************************************************** %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 %~isempty(nonZeroIndx) && length(medianIndx) > (.15*384) catch %try ~ln375 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 catchissue='Ln209' 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 catchissue='Ln209' Exp(expN).Dexp(n).RFmd1pltN= 1; end error='EZexpSel lineAfter 209' end %try ~ln209 end %for d=0:DMnum end % if exist('RF1scanN','var') %********************************************************************************** %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 error='EZexpSel lineAfter 279' end %if RF2scanN doesn't exist this addition to list will be skipped 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 %for d=0:DMnum ln446 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 %if exist('RF2scanN','var') ln445 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %************************************************************************************************* %***********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); try % Determine the dispersed RFs median mean and std if such exist 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 %~isempty(NZrefIndxP) && length(medianIndxDisp) > 3 ln584 catch %try ln565 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 error='EZexpSel lineAfter 565' end %try ~ln565 end %for d=0:DMnum end %for mm=1:length(dMPs) %****************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 % if exist('drf','var') %END OF DISPERSE REFERENCE PLATAES CALCULATIONS AND LIST ADDITIONS %********************************************************************* %Added 17-1023 For User Addition of Gene Composites to ListBox %Expaa{expN,n}= aa; Expbb{expN,n}= bb; %>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> %******************************************************************** %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]); %}