Dear Mr. Pepin,

Thanks a lot for your prompt reply. I saw the read.maimages but just wasn't
sure which file to import.

I will give it a try.

Regards,
S.

On Thu, Nov 19, 2009 at 11:20 PM, Francois Pepin <fpepin@cs.mcgill.ca>wrote:

> Hi Sunny,
>
> To answer the questions in reverse order:
>
> 3- Yes, Limma is a good choice for it. The user's guide is long but full of
> extremely useful information. Going through the relevant sections is
> strongly recommended.
> 2- Agi4x44PreProcess works well if you have human or mouse 4x44 whole
> genome arrays. ArrayQualityMetrics will work anyway. Limma has some
> functions and suggestions as well for that. Again, the Limma user guide is a
> excellent place to start.
> 1- Did I mention Limma before? It read.maimages can read the .txt file from
> the extraction software.
>
> There are of course several ways of doing each of these steps. I mostly
> recommend limma for these steps as it is a reliable and well-documented
> package that should help you get started. Most of the analysis after
> normalization can be done similarly on Agilent and Affy chips.
>
> Francois
>
>
> On 11/19/2009 10:56 PM, Sunny Srivastava wrote:
>
>> Dear Bioconductor Helpers,
>> I have used Bioconductor to analyze Affy chips only, but recently I have
>> to
>> do some analysis for Agilent array. Each array has the two chips with the
>> same sample but the dye swapped (I just made it clear as I saw most of the
>> literature on such arrays with 4 chips).
>>
>> Can any one help me how to:
>> 1 - Import data in Bioconductor? (I mean what is the equivalent of .cel
>> files here - if there is any? I have a few .xml .csv, .txt and .shp files
>> -
>> I am clueless which ones to use and how should I use)
>> 2 - I saw two packages - AgiMicroRNA and Agi4x44PreProcess (the latter
>> seems
>> to be for the 4 chip Agilent array) related to Agilent arrays.
>>      Can anyone point out a good article to read on - how to (completely)
>> analyze such Agilent Arrays - importing, "cleaning up" and analyzing data?
>> 3 - I saw Limma talks about dye swap analysis, so I guess I can use Limma
>> to
>> analyze this data after I am done importing data correctly.
>>
>> I am sorry if I used Agilent array/chip in a wrong way, my knowledge is
>> very
>> limited in this area. I have only analyzed Affy arrays until now.
>>
>> Any help will be appreciated.
>>
>> Thanks,
>> S.
>>
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>>
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