[R] Error in inherits(x, "data.frame") : subscript out of bounds

[kloytyno at mappi.helsinki.fi]

Lainaus "Uwe Ligges" <ligges at statistik.tu-dortmund.de>:

>
>
> On 05.03.2010 15:24, kloytyno at mappi.helsinki.fi wrote:
>> Hi,
>> I have a list p with different size dataframes and length of over 8000.
>> I'm trying to
>> calculate correlations between the rows of dataframes of this list and
>> columns of another
>> dataset (type data.frame also) so that first column is correlated with
>> all the rows in
>> the list dataframe. Some information from another dataset is also
>> included to the final
>> output (all.corrs). This worked a couple of weeks ago when I wrote it
>> but now it seems
>> not to, and gives an error message:
>>
>> Error in inherits(x, "data.frame") : subscript out of bounds
>> In addition: There were 50 or more warnings (use warnings() to see the
>> first 50)
>> warnings()
>> Warning messages: 1: In corrs[j] <- cbind(expressions[j, 1:5],
>> SNP.expr.cor) :
>> number of items to replace is not a multiple of replacement length
>>
>> which indicates that the problem is with getting correlation and other
>> information into
>> corrs. cbind(expressions[j,1:5], SNP.expr.cor) is type data.frame.
>> Changing corrs into
>> matrix, dataframe, list or any other type has not helped.
>>
>> I've updated R from 2.9.0 to the recent version in between. Would anyone
>> have a solution
>> for this problem? I very much appreciate all help.
>>
>> SNP.expr.cor<-NULL
>> all.corrs<-NULL
>> corrs<-NULL
>>
>> for(i in 1:length(p)){
>> dim.exp<-dim(p[[i]])
>> expressions<-p[[i]]
>> expressions.m<-as.matrix(expressions[,6:48])
>> for(j in
>> 1:dim.exp[1]){
>> SNP.expr.cor<-cor(genotypes[,i],expressions.m[j,],use="na.or.complete")
>> corrs[j]<-cbind(expressions[j,1:5], SNP.expr.cor)
>> }
>> all.corrs[i]<-list(cbind(map[i,1:6], corrs))
>> }
>>
>>
>> BR
>> Katja
>>
>
>
> Your example is not reproducible, since we do not have the data.  
> What I guess is that you need to make your objects lists in advance.  
> I cannot try out, but maybe the following works better right away
>
> all.corrs <- vector(mode = "list", length = length(p))
> for(i in seq(along = p)){
>     dim.exp <- dim(p[[i]])
>     corrs <- vector(mode = "list", length = dim.exp[1])
>     expressions <- p[[i]]
>     expressions.m <- as.matrix(expressions[,6:48])
>     for(j in 1:dim.exp[1]){
>         SNP.expr.cor <- cor(genotypes[, i], expressions.m[j, ], use  
> = "na.or.complete")
>         corrs[[j]] <- cbind(expressions[j, 1:5], SNP.expr.cor)
>     }
>     all.corrs[[i]] <- list(cbind(map[i, 1:6]), corrs)
> }
>
>
> Best,
> Uwe Ligges
>
>

Hi, sorry about that, here's a new try:

corrs<-NULL #I've tried everything from vector to matrix to data.frame to list
a<-rnorm(30)
b<-cbind(a,a,a,a,a)
e<-as.matrix(t(b))
c<-c("one", "two", "three", "four", "five")
d<-c("one", "two", "three", "four", "five")
c<-rbind(c,c,c,c,c)

k<-dim(dat)
for(j in 1:k[1]){
	dat.cor<-cor(b[,i],e[j,],use="na.or.complete")
	corrs[j]<-cbind(c[j,1:5], dat.cor)
	}

The trouble seems to be in the inner loop. I'd love to have it as  
data.frame or matrix, not as a list. I think there has been similar  
problems presented here before but I haven't been able to find a  
working solution yet.

BR
Katja Löytynoja



-- 
Katja Löytynoja, M.Sc.
Haartman Institute
Department of Medical Genetics
Biomedicum Helsinki
P.O.Box 63
FIN-00014 University of Helsinki
tel +358-9-19125496
gsm +358-50-4000324
fax +358-9-19125624
e-mail katja.loytynoja at helsinki.fi