[BioC] Reg: T-statistic using limma

[Claus Mayer]

It should be population.goups <- factor(c(rep("LL",3),rep("Control",3))

The way you defined it, each array forms his own group (and thus you have no
degrees of freedom left).

Claus

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Rohit Farmer
> Sent: 16 March 2010 14:00
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Reg: T-statistic using limma
> 
> 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','2Co
> > ntrol2.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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>