[R] stack overflow

[William Noble]

Hello,

I am trying to do an ANOVA on a microarray data set consisting of
22690 elements.  The ANOVA is fine, but when I try to put the data in
a frame in order to exporting it, I get a stack overflow.  I have
found documentation on dynamic memory in R, but not on how to increase
the stack size.  The code I'm using is below.  If anyone has any
suggestions for a workaround here, I'd appreciate it.

Thank you.
Bill Noble

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> invisible(options(echo = TRUE))
> sdata <- read.table("../../data/02-09-03/data.mtx", header=T, row.names=1)
> infection <- gl(2,8,16, label=c("no infection", "infection"))
> labor <- gl(2,4,16, label=c("no labor", "labor"))
> aof <- function(x) {
+   m <- data.frame(infection, labor, x);
+   anova(aov(x ~ infection + labor + infection*labor, m))
+ }
> anovaresults <- apply(sdata, 1, aof)
> pvalues <- data.frame(lapply(anovaresults, function(x) { x["Pr(>F)"][1:3,] }))
Error: protect(): stack overflow
> anovaresults[[1]]
Analysis of Variance Table

Response: x
                Df Sum Sq Mean Sq F value  Pr(>F)  
infection        1   9082    9082  0.2315 0.63907  
labor            1  98722   98722  2.5164 0.13865  
infection:labor  1 143262  143262  3.6517 0.08019 .
Residuals       12 470776   39231                  
---
Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 
> temp <- lapply(anovaresults, function(x) { x["Pr(>F)"][1:3,] })
> length(temp)
[1] 22690
> temp[1]
$"AFFX-BioB-5_at"
         1          2          3 
0.63906707 0.13865289 0.08018914 
> gc(verbose=TRUE)
Garbage collection 62 = 23+6+33 (level 2) ... 
1430471 cons cells free (28%)
17.4 Mbytes of heap free (32%)
          used (Mb) gc trigger  (Mb)
Ncells 3249183 86.8    4953636 132.3
Vcells 4749443 36.3    7025348  53.6
> pvalues <- data.frame(temp)
Error: protect(): stack overflow
> gc(verbose=TRUE)
Garbage collection 63 = 23+6+34 (level 2) ... 
1636368 cons cells free (33%)
19.5 Mbytes of heap free (34%)
          used (Mb) gc trigger  (Mb)
Ncells 3317268 88.6    4953636 132.3
Vcells 4794917 36.6    7353029  56.1