[BioC] Reg: T-statistic using limma

[Rohit Farmer]

thanks Claus

i did as u mentioned and got the results ... but when i am running

results <- decideTests(fit)
and after that

vennDiagram(results)

the vendiagram shows two circles left one shows intercept will the
number of all the genes and the right one population.goupsLLO contains
zero value and the intersection is also not showing contains zero how
can i visualize my results....


On Tue, Mar 16, 2010 at 7:29 PM, Rohit Farmer <rohit.farmer at gmail.com> wrote:
> 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
>
> -------------------------------------------------------------------------
>
> 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
>



-- 
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