Hi James,

Thanks for the suggestion. By using limma2annaffy I am being able to  
get expression intensity in final results but the problem is that a 
separate file is generated for each comparison For Ex. if we have two 
time points and one control than it will generate two different files.

I was thinking of some way to add expression intensity to the results 
from 'decideTests' that has all the comparisons at one place as that is 
important for time series comparison. I think one way to do so is just 
extract the expression intensities from normalized data and add to final 
result file manually using MS Excel.

Besides that I see an error when 'text=TRUE' option is used in 
limma2annafyy:

>limma2annaffy(esetRMA.Reduced, fit2, design, adjust = "none",contrast.matrix, annotation(esetRMA), pfilt = 0.01, fldfilt= 1, text = TRUE, html =FALSE)

You are going to output 3 tables,
With this many genes in each:
  1918 1950 2424
Do you want to accept or change these values? [ a/c ]
a
Warning message:
In chkPkgs(chip) :
   The mouse4302.db package does not appear to contain annotation data.

The error does not appears with just html output.

Thanks

Atul





On 29-Apr-13 9:49 AM, James W. MacDonald wrote:
> Hi Atul,
>
>
> On 4/28/2013 11:55 PM, Atul Kakrana wrote:
>> Hi All,
>>
>> I am using 'affy' and 'limma' to analyze affymetrix data.
>>
>> Simplified code:
>>
>> mydata <- ReadAffy()
>> esetRMA <- rma(mydata)
>> sampletype <- c('1','1','1','2','2','2','3','3','3','4','4','4')
>> group <-factor(sampletype)
>> design<- model.matrix(~0+group)
>> fit <- lmFit(esetRMA, design)
>> contrast.matrix<-makeContrasts(B-A,C-A,D-A, levels=design)
>> fit2<- contrasts.fit(fit,contrast.matrix)
>> fit2 <- eBayes(fit2)
>> results.default <- decideTests(fit2)
>>
>> I get the results without any problem. But what I need is expression 
>> intensity of probes across all samples to be included in the results. 
>> I tried:
>> Intensity <- (2^(exprs(esetRMA)))
>>
>> But cannot fit data to the results
>> fData(results.default) <- Intensity
>>
>> Could somebody please tell me how can include expression intensities 
>> in the 'decideTests' output?
>
> The output from decideTests() is just a matrix of 0 and 1, so you 
> wouldn't want to append anything to that to begin with.
>
> You might take a look at limma2annaffy() in affycoretools, which does 
> essentially what I think you want.
>
> Best,
>
> Jim
>
>
>>
>> AK
>>
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>


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