[BioC] Reg: T-statistic using limma

[Rohit Farmer]

Hi there ... here i am trying to do a moderate t-statistics using
limma i use the following code and got these results but my process in
not able to complete and showing some error at the end

> population.goups <-factor(c('10LLO1.CEL','11LLO2.CEL','12LLO3.CEL','1Control1.CEL','2Control2.CEL','3Control3.CEL')
+ )
> population.goups
[1] 10LLO1.CEL    11LLO2.CEL    12LLO3.CEL    1Control1.CEL
2Control2.CEL 3Control3.CEL
Levels: 10LLO1.CEL 11LLO2.CEL 12LLO3.CEL 1Control1.CEL 2Control2.CEL
3Control3.CEL
> design <- model.matrix (~population.groups)
Error in eval(expr, envir, enclos) : object 'population.groups' not found
> design <- model.matrix (~population.goups)
> design
  (Intercept) population.goups11LLO2.CEL population.goups12LLO3.CEL
population.goups1Control1.CEL
1           1                          0                          0
                         0
2           1                          1                          0
                         0
3           1                          0                          1
                         0
4           1                          0                          0
                         1
5           1                          0                          0
                         0
6           1                          0                          0
                         0
  population.goups2Control2.CEL population.goups3Control3.CEL
1                             0                             0
2                             0                             0
3                             0                             0
4                             0                             0
5                             1                             0
6                             0                             1
attr(,"assign")
[1] 0 1 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$population.goups
[1] "contr.treatment"

> fit <- lmFit(eset, design)
> fit.ebayes <- eBayes(fit)
Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
stdev.coef.lim) :
  No residual degrees of freedom in linear model fits

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Please any help in this regard will be highly appreaciated


Rohit



-- 
Rohit Farmer
M.Tech Bioinformatics
Department of Computational Biology and Bioinformatics
Jacob School of Biengineering and Biotechnology
Sam Higginbottom Institute of Agriculture, Technology and Sciences
(Formerly known as Allahabad Agricultural Institute - Deemed University)
Allahabad, UP, INDIA - 211 007
Ph. No. 9839845093, 9415261403
e-Mail rohit.farmer at gmail.com
Blog http://rohitsspace.blogspot.com