[BioC] Using limma with Agilent array data

[Anh Tran]

Hi,

Thanks for the reply. I'm still not quite understand your reply.

1. Does it mean that this feature is not implemented into limma  
package yet?

2. I want to import the output after extract the intensity (using  
external program) and only use limma for normalization, not the image  
file to scan from scratch. Is there a way to manage that?

Thanks again.

Best,
Anh Tran



On Jun 2, 2008, at 5:56 PM, Sean Davis wrote:

> On Mon, Jun 2, 2008 at 6:26 PM, Anh Tran <popophobia at gmail.com> wrote:
>> Hi all,
>> We've been using Agilent Scanner and Feature Extraction from Agilent.
>>
>> I'm wondering if there's a way to import these data into limma. Out  
>> of the
>> three required input files (GAL file, Targets file, Spot-type  
>> file), we only
>> have GAL file. FE gives us SHP file and a txt file witn compiled  
>> list of
>> probes and its reading. We are doing 2 color microarray btw.
>>
>> If you know any detail, please help us.
>>
>> Also, is it possible to group a certain probes together as one  
>> entity (they
>> are expected to have the same result)? And is it possible to give a  
>> set of
>> probes as normalizing set for limma (set ratio to 1-1)?
>
> Limma offers many options for normalization and choosing probes for
> normalization.  I would definitely put some thought into the rationale
> for using a subset of the probes, though.
>
>> I've been looking through the manual but could not find any  
>> reference about
>> Agilent output file.
>
> You'll need to look at the help, also.  Look at the help for
> read.maimages().  Let us know if that doesn't work by posting the code
> you tried, any errors, and of course the output of sessionInfo().
>
> Sean