[BioC] Agilent Array Analysis Question

Francois Pepin fpepin at cs.mcgill.ca
Fri Nov 20 05:20:46 CET 2009

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.


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.
> 	[[alternative HTML version deleted]]
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