R help - Feb 2008 - Problems reshaping data with cast()

Hi,

I'm trying to cast() some data, but keep on getting the following error...
> norm.all.melted.height <- transform(all.melted.height,
+                                     norm.height = value / ave(value,
SNP, Pool, FUN = max)
+                                     )
Warning messages:
1: In FUN(X[[147L]], ...) :
  no non-missing arguments to max; returning -Inf
2: In FUN(X[[147L]], ...) :
  no non-missing arguments to max; returning -Inf
3: In FUN(X[[147L]], ...) :
  no non-missing arguments to max; returning -Inf
> norm.all.melted.height <- subset(norm.all.melted.height,
select=c("Sample.Name", "SNP", "Pool",
"variable", "norm.height"))
> names(norm.all.melted.height) <- c("Sample.Name",
"SNP", "Pool", "variable", "value")
>
> ## Now reshape the data
> normalised <- cast(norm.all.melted.height, Sample.Name + SNP + Pool ~
value, sum)
Error in rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) :
  negative length vectors are not allowed

Is the error thats occuring with cast() likely to be caused by the
previous warnings?

As far as I can work out rep.int() is called to expand the data based
on the grouping specified (in this case the left hand portion of the
cast formula, i.e.  Sample.Name + SNP + Pool), but how would there be
a negative index in this data?  I had previously melted the data into
this format.

Apologies for not providing a reproducible example, I suspect the
problem lies within the data structure I'm using.

Thanks for reading this question,

Neil

-- 
Email - nshephard at gmail.com / n.shephard at sheffield.ac.uk
Photos - http://www.flickr.com/photos/slackline/

Hi Neil,

I think your cast statement is wrong.  You have

cast(norm.all.melted.height, Sample.Name + SNP + Pool ~ value, sum)

but I think you want

cast(norm.all.melted.height, Sample.Name + SNP + Pool ~ ., sum)

i.e. value never appears in the cast formula.

Hadley

On Feb 7, 2008 7:11 AM, Neil Shephard <nshephard at gmail.com>
wrote:
> Hi,
>
> I'm trying to cast() some data, but keep on getting the following
error...
>
> > norm.all.melted.height <- transform(all.melted.height,
> +                                     norm.height = value / ave(value,
> SNP, Pool, FUN = max)
> +                                     )
> Warning messages:
> 1: In FUN(X[[147L]], ...) :
>   no non-missing arguments to max; returning -Inf
> 2: In FUN(X[[147L]], ...) :
>   no non-missing arguments to max; returning -Inf
> 3: In FUN(X[[147L]], ...) :
>   no non-missing arguments to max; returning -Inf
> > norm.all.melted.height <- subset(norm.all.melted.height,
select=c("Sample.Name", "SNP", "Pool",
"variable", "norm.height"))
> > names(norm.all.melted.height) <- c("Sample.Name",
"SNP", "Pool", "variable", "value")
> >
> > ## Now reshape the data
> > normalised <- cast(norm.all.melted.height, Sample.Name + SNP + Pool
~ value, sum)
> Error in rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) :
>   negative length vectors are not allowed
>
> Is the error thats occuring with cast() likely to be caused by the
> previous warnings?
>
> As far as I can work out rep.int() is called to expand the data based
> on the grouping specified (in this case the left hand portion of the
> cast formula, i.e.  Sample.Name + SNP + Pool), but how would there be
> a negative index in this data?  I had previously melted the data into
> this format.
>
> Apologies for not providing a reproducible example, I suspect the
> problem lies within the data structure I'm using.
>
> Thanks for reading this question,
>
> Neil
>
> --
> Email - nshephard at gmail.com / n.shephard at sheffield.ac.uk
> Photos - http://www.flickr.com/photos/slackline/
>
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
http://had.co.nz/