R help - Feb 2009 - Error in var(x, na.rm = na.rm) : no complete element pairs

Hello all,

I'm trying to calculate the standar desviation and I'm using the
function sd(x,na.rm=TRUE) and I have this error:? Error in var(x, na.rm = na.rm)
: no complete element pairs . Why happen this?, What can I do to solve it?. x is
list of three numbers which I have from a table.


Thanks so much from Spain
Carlos Morales Diego

Hello all,

I'm trying to calculate the standar desviation with sd(x,na.rm=TRUE) and I
don't know why I have this error Error in var(x, na.rm = na.rm) : no
complete element pairs when I try to calculate it, I have been looking for
information about this error but nothing. Why it happens?. What can I do to fix
it?. Thanks so much from Spain


Carlos Morales Diego

Hello,

I still have the same error which I have written in the Subject field, I leave
here the code and I hope you can help me with this:

filter.clones<-function(zz.info,crom.info) 
{ 
    clones.info<-zz.info 
 
    cat("Removing clones which has a flag minor than 0\n") 
    ord <- order(clones.info$Flags) 
    clones.info<- clones.info[ ord, ] 
    #for(j in 1:nrow(clones.info)) 
    #{ 
        del<-0 
        #print(j) 
        del<-which(as.numeric(clones.info$Flags)<0) 
        if (length(del)!=0) 
        { 
            #print(j) 
            clones.info<-clones.info[-del,] 
            #eliminados.info<-clones.info[del,] 
            #if(j==1) 
            #{ 
            #    j<-0 
            #} 
        } 
    #} 
    ##Eliminar levaduras, moscas etc 
    #for(j in 1:nrow(clones.info)) 
    #{ 
 
        del1<-0 
        del1<-grep("mix",clones.info$Name) 
        if (length(del1)!=0) 
        { 
    #        print(j) 
            clones.info<-clones.info[-del1,] 
        } 
    #} 
    #for(j in 1:nrow(clones.info)) 
    #{ 
 
        del2<-0 
        del2<-grep("fly",clones.info$Name) 
        if (length(del2)!=0) 
        { 
    #        print(j) 
            clones.info<-clones.info[-del2,] 
        } 
    #} 
    #for(j in 1:nrow(clones.info)) 
    #{ 
 
        del3<-0 
        del3<-grep("pombe",clones.info$Name) 
        if (length(del3)!=0) 
        { 
    #        print(j) 
            clones.info<-clones.info[-del3,] 
        } 
    #} 
    #for(j in 1:nrow(clones.info)) 
    #{ 
 
        del4<-0 
        del4<-grep("DMSO",clones.info$Name) 
        if (length(del4)!=0) 
        { 
    #        print(j) 
            clones.info<-clones.info[-del4,] 
        } 
    #} 
    #Eliminar los clones que estan unidos por un + o un menos 
    #for(j in 1:nrow(clones.info)) 
    #{ 
        del5<-0 
        del5<-grep("[+]",clones.info$Name) 
        if (length(del5)!=0) 
        { 
    #        print(j) 
            clones.info<-clones.info[-del5,] 
        } 
    #} 
    #for(j in 1:nrow(clones.info)) 
    #{ 
 
        del6<-0 
        del6<-grep("[-]",clones.info$Name) 
        if(length(del6)!=0) 
        { 
    #        print(j) 
            clones.info<-clones.info[-del6,] 
        } 
    #} 
    #for(j in 1:nrow(clones.info)) 
    #{ 
 
        del7<-0 
        del7<-grep("rep",clones.info$Name) 
        if(length(del7)!=0) 
        { 
    #        print(j) 
            clones.info<-clones.info[-del7,] 
        } 
    #} 
        del8<-0 
        del8<-grep("REP",clones.info$Name) 
        if(length(del8)!=0) 
        { 
    #        print(j) 
            clones.info<-clones.info[-del8,] 
        } 
     
 
             
    #cat("Numero de clones:",NROW(clones.info$Name),"\n") 
    #chroms.info<-croms.info(PruebaDefinitiva.obj) 
    #cat("Reordering the chromosomes\n") 
    #ord <- order(chroms.info$picked_off_as_SI_name) 
    #chroms.info<- chroms.info[ ord, ] 
 
 
    #ord <- order(PruebaDefinitiva.obj$crom.info$picked_off_as_SI_name) 
    ##crom.info <- crom.info[ ord, ] 
 
    nrow(clones.info) 
    #a<-PruebaDefinitiva.obj$zz.info 
    #PruebaDefinitiva.obj$zz.info<-0 
    #PruebaDefinitiva.obj$zz.info<-clones.info 
    #PruebaDefinitiva.obj$zz.info 
    clones.info 
 
     
    cat("Reordering the chromosomes\n") 
    ord <- order(crom.info$picked_off_as_SI_name) 
    crom.info<- crom.info[ ord, ] 
    #arch.info<-cbind(arch.info,000) 
    #names(arch.info)[NCOL(arch.info)]<-"Cromosomas" 
 
    clones2.info<-clones.info 
    clones2.info<-cbind(clones2.info,000) 
    names(clones2.info)[NCOL(clones2.info)]<-"Cromosomas" 
    clones2.info 
 
     
    ##A?adir columna con los cromosomas 
    #ncol(arch.info) 
    #arch.info<-arch.info 
    #arch.info<-cbind(arch.info,000) 
    #names(arch.info)[NCOL(arch.info)]<-"Cromosomas" 
    ord <- order(clones2.info$Name) 
    clones2.info<- clones2.info[ ord, ] 
 
    for(i in 1:nrow(clones2.info)) 
    { 
        cat("Processing clon ",i,"\n") 
       
find<-match(clones2.info$Name[i],crom.info$picked_off_as_SI_name,nomatch=0)
        print(find) 
        if((length(find)!=0) &&(find!=0)) 
        { 
            
clones2.info$Cromosomas[i]<-paste(crom.info$current_chromosome[find])
        } 
        find<-0 
    } 
     
        del1<-0 
        del1<-grep("X",clones2.info$Cromosomas) 
        if (length(del1)!=0) 
        { 
    #        print(j) 
            clones2.info<-clones2.info[-del1,] 
        } 
 
        del1<-0 
        del1<-grep("Y",clones2.info$Cromosomas) 
        if (length(del1)!=0) 
        { 
    #        print(j) 
            clones2.info<-clones2.info[-del1,] 
        } 
         
        del1<-0 
        del1<-grep("Un_",clones2.info$Cromosomas) 
        if (length(del1)!=0) 
        { 
    #        print(j) 
            clones2.info<-clones2.info[-del1,] 
        } 
 
        del1<-0 
        del1<-grep("DR",clones2.info$Cromosomas) 
        if (length(del1)!=0) 
        { 
    #        print(j) 
            clones2.info<-clones2.info[-del1,] 
        } 
 
        ord <- order(clones2.info$Cromosomas) 
        clones2.info<- clones2.info[ ord, ] 
        count<-0 
        for(j in 1:nrow(clones2.info)) 
        { 
            nchar(clones2.info$Cromosomas[j]) 
            if(nchar(clones2.info$Cromosomas[j])==0) 
            { 
                count<-count+1 
                #b<-j 
                #arch2.info<-arch2.info[-j,] 
            } 
            #j<-b 
        } 
        for(j in (count+1):nrow(clones2.info)) 
        { 
            clones2.info[j-count,]<-clones2.info[j,] 
        } 
        del<-0 
        del<-which(clones2.info$Cromosomas==0) 
        if (length(del)!=0) 
        { 
            #print(j) 
            clones2.info<-clones2.info[-del,] 
            #if(j==1) 
            #{ 
            #    j<-0 
            #} 
        } 
 
         
        #for(j in 1:nrow(arch2.info)) 
        #{ 
        #    del<-0 
        #    del<-pmatch("0",arch2.info$Cromosomas[j]) 
        #    if((del!=0)&&(length(del)!=0)) 
        #    { 
        #        a<-j 
        #        arch2.info<-arch2.info[-del,] 
        #    } 
        #    j<-a 
        #} 
    clones2.info 
 
    tablesnew.info<-clones2.info 
    Log<-paste(tablesnew.info[,70])
    Log
    cat("Hola holita\n") 
    x<-median(as.numeric(Log),na.rm=TRUE) 
    tablesnew.info<-cbind(tablesnew.info,0)
    cat("Hola holita\n") 
    names(tablesnew.info)[NCOL(tablesnew.info)]<-"LogminusMediana" 
    for(i in 1:nrow(tablesnew.info)) 
    { 
        tablesnew.info$LogminusMediana[i]<-as.numeric(as.character(Log[i]))-x
    } 
    finder<-grep(-x,tablesnew.info$LogminusMediana) 
    tablesnew.info$LogminusMediana[finder]<-as.character(NA) 
 
    tablesnew.info 
 
    triplicadclones.info<-data.frame(paste(tablesnew.info$Name)) 
    names(triplicadclones.info)[1]<-"Name" 
    tripliclones.info<-data.frame(paste(levels(triplicadclones.info$Name))) 
    names(tripliclones.info)[1]<-"Name" 
    tripliclones.info<-cbind(tripliclones.info,000) 
    names(tripliclones.info)[2]<-"LogminusMediana1" 
    tripliclones.info<-cbind(tripliclones.info,000) 
    names(tripliclones.info)[3]<-"LogminusMediana2" 
    tripliclones.info<-cbind(tripliclones.info,000) 
    names(tripliclones.info)[4]<-"LogminusMediana3" 
    cat("Donde co?os esta el error\n") 
    i<-1 
    s<-1 
    del<-0 
    for(i in 1:nrow(tripliclones.info)) 
    { 
        cat(i)        
        d<-tripliclones.info$Name[i] 
        del<-grep(d,tablesnew.info$Name) 
        #print(del) 
        #print(nrow(del)) 
        for(c in 1:NROW(del)) 
        { 
            tripliclones.info[i,c+1]<-tablesnew.info$LogminusMediana[del[c]] 
        } 
    } 
    cat("Estoy aqui") 
    del<-grep("V",names(tripliclones.info)) 
    if(length(del)!=0) 
    { 
        tripliclones.info<-tripliclones.info[,-del] 
    } 
    cat("Y aqui") 
 
    tripliclones.info 
    j<-0
    c<-0
    d<-0
    eliminados<-0
    for(i in 1:NROW(tripliclones.info)) 
    { 
        for(j in 2:4) 
        { 
           
          if(is.na(tripliclones.info[i,j])) 
          { 
            c<-c+1 
          } 
                     
 
            } 
        if(c>=2) 
        { 
            d<-d+1 
            eliminados[d]<-i 
              #gain.info<-gain.info[-i,] 
                c<-0 
        } 
        c<-0 
       } 
    cat("Hola intentando arreglar") 
    tripliclones.info<-cbind(tripliclones.info,000) 
    names(tripliclones.info)[5]<-"Estandar_desviation" 
    for(i in 1:NROW(tripliclones.info)) 
    { 
        de<-0        
        s[1]<-0 
        s[2]<-0 
        s[3]<-0 
        sumatorio<-0 
        for(c in 1:3) 
        { 
            s[c]<-as.numeric(tripliclones.info[i,c+1]) 
         
        }
        cat(s)
        cat(i) 
        de<-sd(s,na.rm=TRUE)
         
        tripliclones.info$Estandar_desviation[i]<-de 
    }
    tripliclones.info
}

The mistake is in de<-sd(s,na.rm=TRUE). Why?. Thanks so much from Spain

Carlos Morales wrote:
> Hello,
> 
> I still have the same error which I have written in the Subject field, I
leave here the code and I hope you can help me with this:
> 
[removed]

the lengthy code example does not make it easier to help you, in particular
without the
data you used. All the commented out code should have been removed before
posting.
My guess is that you use R < 2.8.0 and generate a vector s which contains
only NAs.
Try to inspect your function filter.clones by putting a browser()
call somewhere before the sd() call and run it again.
See ?browser and ?trace.

And you could vectorize this (and other parts), e.g.
the last loop would be rewritten as

tripliclones.info$Estandar_desviation <- apply(tripliclones.info[ ,2:4], 1,
function(x)
sd(as.numeric(x), na.rm=TRUE))

Regards, Matthias


R version 2.7.1 (2008-06-23)
> b <- rep(NA,4)
> sd(b)
Error in var(x, na.rm = na.rm) : missing observations in
cov/cor
> sd(b, TRUE)
Error in var(x, na.rm = na.rm) : no complete element pairs


R version 2.8.1 (2008-12-22)
> b<- rep(NA,4)
> sd(b)
[1] NA
> sd(b, TRUE)
[1] NA

-- 
Matthias Burger                     Project Manager/ Biostatistician
Epigenomics AG    Kleine Praesidentenstr. 1    10178 Berlin, Germany
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