[R-sig-ME] large dataset - lmer2 vector size specified is too large

[florian bw]

Hi,

I want to fit mRNA expression data to sex.

I have the following values:
  expr:     expression value (for gene/person)
  affyID:   gene ID
  cephID: person ID
  sex

with 224 genes and 195 persons, therefore 43,680 data points. Both
with the nlme and the lme4 package i get errors. I tried it with R 2.4
and 2.5, and the newest package versions.

I have a 64-machine with 8GB RAM. Is the dataset simply too large? I
already cut it down and would actually be glad if I could do the
calculation with ~ 8000x250 data points.

Thank you for your help.

Florian Breitwieser
UNSW Sydney
Systems Biolgy

---------------------------------------------------

> sessionInfo()
R version 2.5.0 Under development (unstable) (2007-02-26 r40806)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
[7] "base"

other attached packages:
       lme4      Matrix     lattice        nlme
"0.9975-13" "0.9975-11"   "0.14-16"    "3.1-79"


-----------------------------------------------------

> library(lme4)
> sex.lme <- lmer2(expr ~ affyID*sex + affyID|cephID,data=ds.n)
Error in vector("double", length) : vector size specified is too large


------------------------------------------------------

> library(nlme)
> sex.lme <- lme(expr ~ affyID*sex,random=~affyID|cephID,data=ds.n)
Error: cannot allocate vector of size 4.7 Gb
> gc()
          used (Mb) gc trigger   (Mb)   max used   (Mb)
Ncells  829281 44.3    5714627  305.2   10890793  581.7
Vcells 1881820 14.4 1034019068 7889.0 1103035467 8415.5


Another time I got the following message:
> sex.lme <- lme(expr ~ affyID*sex,random=~affyID|cephID,data=ds.n)

 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: lme.formula(expr ~ affyID * sex, random = ~affyID | cephID, data = ds.n)
 2: lme(expr ~ affyID * sex, random = ~affyID | cephID, data = ds.n)