[BioC] Reg: T-statistic using limma

[Rohit Farmer]

Thanks Claus once again

u sorted out my problem actually i want to look for differential
expression ... and i got it i believe ... actually right now i am
graduate student only and dont know much theory behind microarray data
analysis ...i am following a paper as a protocol and referring to
manuals ...

Next i want to go for clustering using different algorithms its the
next objective of my semester project can u suggest me which library
to use ... and a flow chart sort of ... you have been great help to me
i was struggling since morning .. GOD bless


Thanks

Rohit

On Tue, Mar 16, 2010 at 8:45 PM, Rohit Farmer <rohit.farmer at gmail.com> wrote:
> 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
>



-- 
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