[BioC] Using limma with Agilent array data

[Sean Davis]

On Mon, Jun 2, 2008 at 10:31 PM, Anh Tran <popophobia at gmail.com> wrote:
> 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?

Hi, Anh.  Again, you'll want to read the help for read.maimages.  You
can do this by loading the limma package and then typing:

help(read.maimages)

In particular, look at the "source" argument.  And, yes, this function
reads the .txt file after feature extraction.  If you need a list of
all the functions for which there is help in limma, you can type:

help(package=limma)

Again, if you have further questions, please include the code you
tried, any errors, and for ANY questions to the list, the output from
the sessionInfo() function.

Hope that clarifies.

Sean

> 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
>
>