Hi James,
I used row.names =1 as suggested by you and Martin.I did not get any error
and included these steps.
>fit_pair <- eBayes(fit_pair)
> topTable(fit_pair, coef="TreatT")
and got a list
                 ID             logFC    AveExpr         t
P.Value            adj.P.Val         B
114659 3807490 1938.54365 4407.17510  93.62245 5.066916e-06 0.6773048
-4.555623
93178  3536336   89.25101   76.95120  57.13317 2.044799e-05 0.9313141
-4.555652
15914  2523632   85.55042   75.01551  48.02453 3.339131e-05 0.9313141
-4.555671
82198  3401197  114.17548  185.84179  46.26832 3.709470e-05 0.9313141
-4.555677
82576  3405396 -112.96339  214.93046 -43.24963 4.487733e-05 0.9313141
-4.555687
44334  2900091  227.49472  197.41073  39.63887 5.739658e-05 0.9313141
-4.555702
1373   2330451   76.19923  155.62751  38.99148 6.012674e-05 0.9313141
-4.555706
124852 3923312   62.34274   96.81574  38.91146 6.047631e-05 0.9313141
-4.555706
6531   2398894  279.18572  372.08333  38.28233 6.332302e-05 0.9313141
-4.555709
34618  2772414 -162.60332  150.62089 -36.12449 7.458547e-05 0.9313141
-4.555722

Here I have considered only 6 samples and tumor vs normal as I would like
to try the whole dataset in 64 bit machine( due to memory issues) later if
this code works.
My actuall intention is to design the paired ttest for multiple subgroups
for 80 patients with tumor and their respective normal samples(80). (with
in brackets are the no of subjects)
Subgroups:

Group(160)-   Tumor(80),     Normal(80)
Gender(80)-   Female(27),    Male(53)
Stage(80)-     I(4),      II(7),        III(54),        IV(15)
Age(77)->=55(53),   <55(24), unknown(3)

How to include these conditions, is it by just mentioning in the targets
file? and how do I have to change the rest to get this design?
Is it possible to perform this in one go or should it be performed as
different conditions indiviually?
waiting for your suggestions,
Thanks,
Viritha

On Tue, Jan 17, 2012 at 4:49 PM, James W. MacDonald
<jmacdon@med.umich.edu>wrote:

> Hi Viritha,
>
>
> On 1/17/2012 4:36 PM, viritha k wrote:
>
>> 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<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)
>>>
>>
> At the very least you should add a row.names = 1 to your call to
> read.table(). You want the ID to be the row.names of your matrix, not the
> first column.
>
> Since the dimensions of your matrix don't match the number of rows of your
> design matrix, I would expect a different error,
>
> Error in lm.fit(design, t(M)) : incompatible dimensions
>
> So there might be something else wrong. You don't show the final design
> matrix, so no telling.
>
> Best,
>
> Jim
>
>
>   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
>>
>>        [[alternative HTML version deleted]]
>>
>> ______________________________**_________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor>
>> Search the archives: http://news.gmane.org/gmane.**
>> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
>
> ************************************************************
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues
>

	[[alternative HTML version deleted]]

