Thanks a lot !! Everything went pretty well .. I hope the analysis also goes smoothly :D Best Regards, S. On Thu, Nov 19, 2009 at 11:36 PM, Sunny Srivastava <research.baba@gmail.com>wrote: > 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. >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]