Hi group,
I am trying to perform paired t-test for 6 samples which are paired one is
from normal tissue of the subject and the other is tumor tissue of the same
subject.
I am following the code as mentioned in the Limma User guide,p.40,8.3
Paired Samples)

Code:
>source("http://bioconductor.org/biocLite.R")
>biocLite("limma")
>library(limma)
>targets<-readTargets("targets.txt")
>head(targets)
   FileName Pair Treatment
1 GSM675890    1         N
2 GSM675891    1         T
3 GSM675892    2         N
4 GSM675893    2         T
5 GSM675894    3         N
6 GSM675895    3         T

>eset<-as.matrix(read.table("6samples.txt",sep='\t',header=TRUE,colClasses=c(rep('numeric',7)),nrow=133673))
>head(eset)

 ID_REF GSM675890 GSM675891 GSM675892 GSM675893 GSM675894 GSM675895
[1,] 2315129  30.32278  20.42571   7.60854  17.15130  14.57533  22.22889
[2,] 2315145  12.74657   6.30117  11.43528   4.10696   3.12693  10.96096
[3,] 2315163 175.96267 125.77725  52.19822 102.07567 116.91966 174.41690
[4,] 2315198   6.57030   1.85541   3.34829   1.13516   0.34278   1.83917
[5,] 2315353  88.49511  48.77128  50.60524  62.92448  47.10977  45.06430
[6,] 2315371   2.01707   1.90644 536.07636   2.21359   0.00212   0.43249

>Pair<-factor(targets$Pair)
>Treat<-factor(targets$Treatment,levels=c("N","T"))
>design<-model.matrix(~Pair+Treat)
>fit_pair<-lmFit(eset,design)
Error: (subscript) logical subscript too long

>sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] limma_3.10.1        BiocInstaller_1.2.1
loaded via a namespace (and not attached):
[1] tools_2.14.1
Please suggest as to where is the issue?
Thanks,
Viritha

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