---------- Forwarded Message ----------
Date: 18 September 2009 19:24 +0100
From: A Singh <bz...@bristol.ac.uk>
To: William Dunlap <wdun...@tibco.com>
Subject: RE: [R] Error: length(f1) == length(f2) is not TRUE
Yup, they are all factors- and its still doesn't work.
Getting to the stage where I can use 'summary()' is the problem- the error
stalls the process before a summary can be output.
I tried the same code, but using 'family' and P1L55 as independent random
factors, and that works.
(I actually tried this with a new marker P1L74)
try(fit<-lmer(peg.no~1 + (1|family) + (1|P1L74), na.action=na.exclude))
summary(fit)
Linear mixed model fit by REML
Formula: peg.no ~ 1 + (1 | family) + (1 | P1L74)
AIC BIC logLik deviance REMLdev
2981 2997 -1487 2976 2973
Random effects:
Groups Name Variance Std.Dev.
family (Intercept) 87.86380 9.37357
P1L74 (Intercept) 0.48815 0.69868
Residual 92.11681 9.59775
Number of obs: 390, groups: family, 57; P1L74, 2
Fixed effects:
Estimate Std. Error t value
(Intercept) 96.40 1.49 64.71
..but the nested random effect ..(1|family/P1L74).. is where the error
occurs. And its the same error.
Error : length(f1) == length(f2) is not TRUE
In addition: Warning messages:
1: In P1L55:family :
numerical expression has 390 elements: only the first used
2: In P1L55:family :
numerical expression has 390 elements: only the first used
My design is a very unbalanced one. Do you think that can be the problem?
--On 18 September 2009 09:11 -0700 William Dunlap <wdun...@tibco.com> wrote:
Look at the output of summary(vcdf) and make sure
that 'family' and 'P1L55' columns are factors. Perhaps
columns 4:13 did not include them.
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
-----Original Message-----
From: A Singh [mailto:aditi.si...@bristol.ac.uk]
Sent: Friday, September 18, 2009 9:03 AM
To: William Dunlap; r-help@r-project.org
Subject: RE: [R] Error: length(f1) == length(f2) is not TRUE
Hi Bill,
Thanks, I did try out what you suggested but it doesn't seem to work.
I get the same error again.
There's obviously something here that I don't get. Need to
figure it out.
Aditi
--On 18 September 2009 08:34 -0700 William Dunlap
<wdun...@tibco.com> wrote:
>> From: r-help-boun...@r-project.org
>> [mailto:r-help-boun...@r-project.org] On Behalf Of A Singh
>> Sent: Friday, September 18, 2009 4:42 AM
>> To: r-help@r-project.org
>> Subject: [R] Error: length(f1) == length(f2) is not TRUE
>>
>>
>> Dear R users,
>>
>> I am trying to fit an lmer model with only random effects
>> which is giving
>> me the following error:
>>
>> Error : length(f1) == length(f2) is not TRUE
>> In addition: Warning messages:
>> 1: In P1L55:family :
>> numerical expression has 390 elements: only the first used
>> 2: In P1L55:family :
>> numerical expression has 390 elements: only the first used
>>
>>
>> I am trying to extract variance components for a phenotype
>> 'peg.no', using
>> the variable 'family' and a marker column 'P1L55' (which is
>> categorical and
>> has 2 levels- 0 and 1), as random effects. There are no
fixed effects.
>>
>> The code I used is as follows:
>>
>> vc<-read.table(...)
>>
>> vcdf<-data.frame(vc)
>> colms<-(vc)[4:13] ##these are the markers
>> lapply(colms,factor)
>
> Note that you did not change columns 4:13 of vcdf to factors:
> you changed copies of them to factors. Do
> vcdf[4:13] <- lapply(vcdf[4:13], factor)
> and lmer should be happier.
>
> Bill Dunlap
> TIBCO Software Inc - Spotfire Division
> wdunlap tibco.com
>
>>
>> try(fit<-lmer(peg.no~1 + (1|family/P1L55),
>> na.action=na.include, data=vcdf))
>>
>>
>> I thought that putting the data into a dataframe would help,
>> along with the
>> na.exclude command, because there is a lot of missing data in
>> patches which
>> I have replaced with NA's, but I don't know how to fix this
>> error at all.
>>
>> Its a bit urgent, and any help is hugely appreciated.
>>
>> The data files are at:
>>
>>
>> <http://www.4shared.com/file/131980362/460bdafe/Testvcomp10.ht
>> ml> (excel)
>> http://www.4shared.com/file/131980512/dc7308b/Testvcomp10.html
>> (txt)
>>
>>
>> Cheers,
>> Aditi
>>
>> ----------------------
>> A Singh
>> aditi.si...@bristol.ac.uk
>> School of Biological Sciences
>> University of Bristol
>>
>> ______________________________________________
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
----------------------
A Singh
aditi.si...@bristol.ac.uk
School of Biological Sciences
University of Bristol
----------------------
A Singh
aditi.si...@bristol.ac.uk
School of Biological Sciences
University of Bristol
---------- End Forwarded Message ----------
----------------------
A Singh
aditi.si...@bristol.ac.uk
School of Biological Sciences
University of Bristol
______________________________________________
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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.
