[BioC] Limma: Nimblegen array data import?

[Mark Robinson]

Dave,

I encourage you to read the limma documentation.

Cut and paste from a not so recent version of the limma user's guide  
(though it may be the same as the recent one, i haven't checked):

 > design <- model.matrix(~ -1+factor(c(1,1,1,2,2,3,3,3)))
 > colnames(design) <- c("group1", "group2", "group3")
 > fit <- lmFit(eset, design)

In your case, just replace the 'eset' with your table of intensities  
and modify the bit in the 'model.matrix' command to match the columns  
to your situation.

You could probably define a targets file also.

Cheers,
Mark

On 29/11/2007, at 3:12 PM, Dave Berger wrote:

> Hi Mark
> how do I define for limma which column is which treatment? - do I  
> need to define this using a targets file?
> thanks
> Dave
>
> Quoting Mark Robinson <mrobinson at wehi.EDU.AU>:
>
>>
>> How about just running 'limma' on the table of normalized  
>> expression values?
>>
>> In ?lmFit, the object which gets operated on doesn't have to be an  
>> exprSet.
>>
>> M.
>>
>> On 29/11/2007, at 2:52 PM, Dave Berger wrote:
>>
>>> previously, I have used limma for 2 colour array analysis.
>>> I now have a new data set from Nimblegen arrays in which RMA
>>> normalization has been completed and I wish to identify  
>>> differentially
>>> expressed genes from the allcalls.txt file which is a table of
>>> expression values for all the treatments in one file
>>> Question:
>>> if I wish to do a single channel analysis in "limma", I would
>>> appreciate suggestions on importing this data ie. how do I  
>>> convert the
>>> data to an "exprSet" object?
>>>
>>> thanks
>>> Dave Berger
>>>
>>>
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>
>
>
> -- 
> ~~
> Dave Berger, PhD
> Professor, Plant Science
> Room 6-26,Agricultural Sciences Building
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